Plant Comparative Genomics

Trichomes in Chickpea serve as a possible defence mechanism against movement and Ovi-positioning of various stages of insect pests. This research was planned to assess the density and length of trichomes on the leaves and pods of forty-two genotypes alongside two local control varieties. Two types of trichomes were identified: non-glandular on leaves and glandular on pods. Only a small number of glandular trichomes were found on leaves, while very few non-glandular trichomes were present on pods. The highest density of non-glandular trichomes on leaves (26.33 trichomes/mm2) was recorded in the chickpea genotype KGG 22016. The lowest count of glandular trichomes on the pods was noted for Genotype KGG 22005 (7.67 glandular trichomes per mm2). In the case of leaves, KGG 22007 (347.23 µm) and KGG 22004 (301.53 µm) exhibited the highest length of non-glandular trichomes, respectively. Conversely, genotypes KGG 22005 (564.97 µm) and KGG 22004 (538.33 µm) showed the greatest glandular trichome length in the pods. The density of non-glandular trichomes on leaves displayed a positive correlation with the number of eggs, the larval survival rate, and the overall larval population, while it had a negative correlation with the percentage of pod damage. On the other hand, the density of glandular trichomes on pods revealed a notable positive correlation with the number of eggs, the H. armigera larval population, larval survival, and pod damage.

The genome of the model cyanobacterium, Synechococcus sp. PCC 7002, encodes two paralogs of CruA-type lycopene cyclases, SynPCC7002_A2153 and SynPCC7002_A0043, which are denoted cruA and cruP, respectively. Unlike the wild-type strain, a cruA deletion mutant is light-sensitive, grows slowly, and accumulates lycopene, c-carotene, and 1-OH-lycopene; however, this strain still produces b-carotene and other carotenoids derived from it. Expression of cruA from Synechocystis sp. PCC 6803 (cruA 6803) in Escherichia coli strains that synthesize either lycopene or c-carotene did not lead to the synthesis of either c-carotene or b-carotene, respectively. However, expression of this orthologous cruA 6803 gene (sll0147) in the Synechococcus sp. PCC 7002 cruA deletion mutant produced strains with phenotypic properties identical to the wild type. CruA 6803 was purified from Synechococcus sp. PCC 7002 by affinity chromatography, and the purified protein was pale yellow-green due to the presence of bound chlorophyll (Chl) a and b-carotene. Native polyacrylamide gel electrophoresis of the partly purified protein in the presence of lithium dodecylsulfate at 4°C confirmed that the protein was yellow-green in color. When purified CruA 6803 was assayed in vitro with either lycopene or c-carotene as substrate, b-carotene was synthesized. These data establish that CruA 6803 is a lycopene cyclase and that it requires a bound Chl a molecule for activity. Possible binding sites for Chl a and the potential regulatory role of the Chl a in coordination of Chl and carotenoid biosynthesis are discussed.

Selaginella tarmariscina is a resurrection plant and we have cloned several genes for dehydration in S. tarmariscina through differential display. One of the gene (DQ471954) which has 68% homology with Arabidopsis thaliana thylakoid lumen 18.3 kDa protein (TLP18.3) gene. This gene has a domain of unknown function (DUF477) which is a family of uncharacterized protein. The expression pattern of the A. thaliana TLP18.3 reveals that mRNA expression and protein accumulation up-regulated during dehydration. The protein coding region of A. thaliana TLP18.3 gene consist of 3 exons and 4 introns encoding 285 amino acid with putative chloroplast transit peptide (cTP) target sequence at N-terminal. GFP fusion protein with N-terminal 80 amino acid residue reveals that this fusion protein is localized into chloroplast. Our data strongly suggest that A. thaliana TLP18.3 gene has important role in dehydration process.

This report describes the cloning and expression of a gene lycopene epsilon cyclase, (LCYE) from Camellia sinensis var assamica which is a precursor of the carotenoid lutein in tea. The 1982 bp cDNA sequence with 1599 bp open reading frame of LCYE was identified from an SSH library constructed for quality trait in tea. 5' and 3' RACE (rapid-amplification of cDNA ends) was done to clone the full length cDNA of LCYE. Homology studies showed that the deduced amino acid sequence of LCYE gene had the highest sequence identity of up to 84% with Vitis vinefera. The cloned gene was successfully expressed in a PET based Escherichia coli expression system. The size of the expressed protein was 59615 Daltons. A suppression subtractive library was constructed using a quality clone H3111 (tester) and a garden series clone T3E3 (driver).

Wild grapevine-Vitis vinifera subsp. sylvestris-ancestors of cultivated grapevines are the main players in understanding the molecular bases of the grapevine domestication process. The goal of the presented research was to assess the genetic diversity of wild grapevine samples from several regions encompassing Europe (Spain, France, Germany, Hungary, Greece), the Mediterranean basin (Algeria, Tunisia, Morocco), and South Caucasus (Georgia), using a complete chloroplast DNA sequencing. The results suggest the existence of three different chloroplast DNA haplotypes reflecting the geographical distribution of the analyzed samples. This study represents the first report focused on analysis of a wide range of wild grapevine samples (Vitis vinifera subsp. sylvestris), applying next-generation technologies, and tracing the grapevine ancestry.

Rice landraces are vital genetic resources for agronomic and quality traits but the undeniable collection of Kerala landraces remains poorly delineated. To effectively conserve, manage, and use these resources, understanding the genomic structure of germplasm is essential. Genotyping by sequencing (GBS) enables identification of an immense number of single nucleotide polymorphism (SNP) and insertion deletion (InDel) from 96 rice germplasm. In the present study, a total of 16.9 × 10 7 reads were generated, and among that 16.3 × 10 7 reads were mapped to the indica reference genome. Exploring GBS data unfolded a wide genomic variations including 82,59,639 SNPs and 1,07,140 Indels. Both neighbor-joining tree and principal coordinate analysis with InDel markers revealed the selected germplasm in this study as highly diverse in structure. We assembled unmapped reads which were further employed for gene ontology analysis. These unmapped sequences that are generally expelled from subsequent studies of GBS data analysis may exist as an unexplored resort for several novel significant biological findings. The discovery of SNPs from the haplotyping results of GS3 and GIF1 genes provided insight into marker-assisted selection based on grain size and yield and can be utilized for rice yield improvement. To our knowledge, this is the first report on structural variation analysis using the GBS platform in rice landraces collected from Kerala. Genomic information from this study endows with valuable resources for perceptive rice landrace structure and can also facilitate sequencing-based molecular breeding.

DNA sequence diversity was investigated in three plastid regions (the trnH-psbA intergenic spacer, accD-psaI intergenic spacer and the rpl16 intron) in a group of 40 wild grape (Vitis vinifera subsp. sylvestris) samples from the South Caucasus. This group included 22 samples from Georgia, 9 samples from Azerbaijan, 2 samples from Armenia and 7 samples from Turkey. The South Caucasus region is widely believed to be the area in which grape domestication began, and the study of genetic diversity in this region is viewed as key to understanding grape domestication in general. Four plastid haplotypes are evident in the 40 samples, and are designated by their character states at each of the 4 polymorphic positions: AAAT-22 samples, ATTT-6 samples, GTAC-1 sample, and ATAT-11 samples. The AAAT haplotype is restricted to Georgia and Azerbaijan, the ATAT haplotype is distributed across the entire study area, the ATTT haplotype is distributed in the southern part of the study area from the Black Sea to the Caspian Sea. The single GTAC haplotype was only found in southwestern Georgia. The AAAT haplotype is restricted to both wild (V. vinifera subsp. sylvestris) and cultivated (V. vinifera subsp. vinifera) grape samples from the Caucasus. This observation and the presence of all other plastid haplotypes observed in a previous study of worldwide grape cultivars highlight both unique and high levels of genetic variation in wild grape (V. vinifera subsp. sylvestris) from the greater Caucasus region. K e y w o r d s : Grape DNA, Vitis vinifera subsp. sylvestris, trnH-psbA intergenic spacer, accD-psaI intergenic spacer, rpl16 intron, DNA sequencing.

The meagre, Argyrosomus regius, has recently become a species of increasing economic interest for the Mediterranean aquaculture and there is ongoing work to boost production efficiency through selective breeding. Access to the complete genomic sequence will provide an essential resource for studying quantitative trait-associated loci and exploring the genetic diversity of different wild populations and aquaculture stocks in more detail. Here, we present the first complete genome for A. regius, produced through a combination of long and short read technologies and an efficient in-house developed pipeline for assembly and polishing. Scaffolding using previous linkage map data allowed us to reconstruct a chromosome level assembly with high completeness, complemented with gene annotation and repeat masking. The 696 Mb long assembly has an N50 = 27.87 Mb and an L50 = 12, with 92.85% of its length placed in 24 chromosomes. We use this new resource to study the evolution of the meagre geno...

The meagre, Argyrosomus regius, has recently become a species of increasing economic interest for the Mediterranean aquaculture and there is ongoing work to boost production efficiency through selective breeding. Access to the complete genomic sequence will provide an essential resource for studying quantitative trait-associated loci and exploring the genetic diversity of different wild populations and aquaculture stocks in more detail. Here, we present the first complete genome for A. regius, produced through a combination of long and short read technologies and an efficient in-house developed pipeline for assembly and polishing. Scaffolding using previous linkage map data allowed us to reconstruct a chromosome level assembly with high completeness, complemented with gene annotation and repeat masking. The 696 Mb long assembly has an N50 = 27.87 Mb and an L50 = 12, with 92.85% of its length placed in 24 chromosomes. We use this new resource to study the evolution of the meagre geno...

While the gargantuan multi-nation effort of sequencing T. aestivum gets close to completion, the annotation process for the vast number of wheat genes and proteins is in its infancy. Previous experimental studies carried out on model plant organisms such as A. thaliana and O. sativa provide a plethora of gene annotations that can be used as potential starting points for wheat gene annotations, proven that solid cross-species gene-to-gene and protein-to-protein correspondences are provided. DNA and protein sequences and corresponding annotations for T. aestivum and 9 other plant species were collected from Ensembl Plants release 22 and curated. Cliques of predicted 1-to-1 orthologs were identified and an annotation enrichment model was defined based on existing gene-GO term associations and phylogenetic relationships among wheat and 9 other plant species. A total of 13 cliques of size 10 were identified, which represent putative functionally equivalent genes and proteins in the 10 pl...

Worldwide genome sequencing efforts for plants with medium and large genomes require identification and visualization of orthologous genes, while their syntenic conservation becomes the pinnacle of any comparative and functional genomics study. Using gene models for 20 fully sequenced plant genomes, including model organisms and staple crops such as Aegilops tauschii Coss., Arabidopsis thaliana (L.) Heynh., Brachypodium distachyon (L.) Beauv., turnip (Brassica rapa L.), barley (Hordeum vulgare L.), rice (Oryza sativa L.), sorghum [Sorghum bicolor (L.) Moench], wheat (Triticum aestivum L.), red wild einkorn (Triticum urartu Tumanian ex Gandilyan), and maize (Zea mays L.), we computationally predicted 1,021,611 orthologs using stringent sequence similarity criteria. For each pair of plant species, we determined sets of conserved synteny blocks using strand orientation and physical mapping. Gene ontology (GO) annotations are added for each gene. Plant Orthology Browser (POB) includes three interconnected modules: (i) a gene-order visualization module implementing an interactive environment for exploration of gene order between any pair of chromosomes in two plant species, (ii) a synteny visualization module providing unique interactive dot plot representations of orthologous genes between a pair of chromosomes in two distinct plant species, and (iii) a search module that interconnects all modules via free-text search capability with online as-you-type suggestions and highlighting that allows exploration of the underlining information without constraint of interface-dependent search fields. The POB is a web-based orthology and annotation visualization tool, which currently supports 20 completely sequenced plant species with considerably large genomes and offers intuitive and highly interactive pairwise comparison and visualization of genomic traits via gene orthology.

While the gargantuan multi-nation effort of sequencing T. aestivum gets close to completion, the annotation process for the vast number of wheat genes and proteins is in its infancy. Previous experimental studies carried out on model plant organisms such as A. thaliana and O. sativa provide a plethora of gene annotations that can be used as potential starting points for wheat gene annotations, proven that solid cross-species gene-to-gene and protein-to-protein correspondences are provided. DNA and protein sequences and corresponding annotations for T. aestivum and 9 other plant species were collected from Ensembl Plants release 22 and curated. Cliques of predicted 1-to-1 orthologs were identified and an annotation enrichment model was defined based on existing gene-GO term associations and phylogenetic relationships among wheat and 9 other plant species. A total of 13 cliques of size 10 were identified, which represent putative functionally equivalent genes and proteins in the 10 pl...

Background Kernel row number (KRN) is an important yield component trait with a direct impact on the productivity of maize. The variability in KRN is influenced by the inflorescence meristem size, which is determined by the CLAVATA-WUSCHEL pathway. A CLAVATA receptor-like protein, encoded by the FASCIATED EAR2 (fea2gene), enhances the growth of inflorescence meristem and is thus involved in the determination of KRN. The amplicon sequencing-based method was employed to dissect the allelic variation of the fea2 gene in tropical field corn. Methodology/Principal finding Amplicon-based sequencing of AI 535 (Low KRN) and AI 536 (High KRN) was undertaken for the gene fea 2 gene that codes for KRN in maize. Upon multiple sequence alignment of both sequences, A to T transversion at the 1311 position was noticed between Low KRN and High KRN genotypes resulting in different allelic forms of a fea2 gene in tropical maize. An allele-specific primer 1311 fea2.1 was designed and validated that ca...

The introduction of mechanized agricultural practices after the Second World War and the use of productive hybrids led to a gradual disappearance of local maize varieties. However, 13 landraces are still cultivated in North-Western Italy, in the Lombardy region; those that are cultivated in mountainous areas (roughly up to 1200 m in altitude) are often characterized by the pointed shape of their seeds (i.e., “Nero Spinoso”, “Rostrato Rosso di Rovetta”, “Spinato di Gandino” and “Scagliolo di Carenno”) and the presence of pigments (i.e., “Nero Spinoso”, “Rostrato Rosso di Rovetta”). The pointed shape of the seeds is an ancient characteristic of maize-ancestors, which negatively affects the yield by not allowing optimal “filling” of the ear. This study reports work on four different Italian varieties of pointed maize in order to assess the genetic bases of the “pointed character” and to try to explain the reasons for this adaptation to the mountain environment. The data obtained by gen...

Oil palms are important commodity crop in Malaysia as major contributor to agriculture sector. Thus, the need for better yield production is urgent to accommodate rising local and global demand while reducing the land expansion for oil palm plantation. This can be achieved by identifying the agronomical important traits in oil palm using comparative genomic approach. In this study, gene related to plant height, fruit development and fruit ripening in oil palm were predicted by comparing Elaeis guineensis genome sequence with Arabidopsis thaliana and Solanum lycopersicum genome sequence. The model plant chosen are based on its special attribute such as completely sequenced and fleshy fruit model. The analysis begun with orthology analysis using InParanoid, and SonicParanoid. There are 9,624 orthologous genes identified common among species selected. The reformatted orthologous genes were then annotated with Gene Ontology (GO) using Blast2GO program. The process of annotation include ...

Whereas breeders have exploited diversity in maize for yield improvements, there has been limited progress in using beneficial alleles in undomesticated varieties. Characterizing standing variation in this complex genome has been challenging, with only a small fraction of it described to date. Using a population genetics scoring model, we identified 55 million SNPs in 103 lines across pre-domestication and domesticated Zea mays varieties, including a representative from the sister genus Tripsacum. We find that structural variations are pervasive in the Z. mays genome and are enriched at loci associated with important traits. By investigating the drivers of genome size variation, we find that the larger Tripsacum genome can be explained by transposable element abundance rather than an allopolyploid origin. In contrast, intraspecies genome size variation seems to be controlled by chromosomal knob content. There is tremendous overlap in key gene content in maize and Tripsacum, suggesting that adaptations from Tripsacum (for example, perennialism and frost and drought tolerance) can likely be integrated into maize. Maize nucleotide diversity is near the upper limit of that estimated for crops and is an order of magnitude higher than in humans 1,2. However, this genetic diversity not only arises from SNPs and small insertions-deletions (indels) but also from larger structural variations 3-5. Additionally, homeologous segments in this paleopolyploid contribute to genome complexity. Nearly 85% of the maize reference genome sequence is annotated as transposable elements 6,7 , and cycles of transposable element invasion, activity and loss 8 , combined with the ability of these elements to shuffle gene fragments, have undoubtedly left a profound impact on the genome. Recent estimates suggest that the reference B73 sequence may capture only ~70% of the low-copy gene fraction of maize inbred lines 9 , with both genes and transposable elements occupying the unshared sequence space 10. Consequently, in addition to SNPs and small indels, structural variations in the form of copy-number variations, presence/absence variations and movement of transposable elements 3-5 contribute substantially to the genetic diversity in maize. Characterizing this diversity-in particular, at a sufficient density to drive genome-wide association studies (GWAS) or genomic selection-has been technically challenging. Here, through whole-genome surveys using sequencing-bysynthesis technology, we have conducted a comprehensive characterization of genetic variation across 103 inbred lines representing a wide breadth of the Z. mays lineage, comprising 60 improved maize lines, including the parents of the maize nested association mapping (NAM) population 11 , 23 maize landraces and 19 wild relatives (17 Z. mays ssp. parviglumis and 2 Z. mays ssp. mexicana)

Festuca is one of the largest genera of the grass family, which has more than 600 species with different ploidy levels. The aim of this study was to estimate the genetic diversity within 22 populations of three species of Festuca (Festuca arundinacea, F.rubra and F.ovina) using a seed storage protein electrophoresis pattern. These species showed a significant variation in the number of protein bands from 5-13. The highest number of bands was found in G17 (F.rubra) and the lowest number of protein bands was in G5 (F.ovina). Band number 14 was only observed in G3. It is suggested that this band can be considered as a specific band for the identification of this genotype. According to the results of AMOVA analysis, there is a high level of genetic diversity within the species rather than between species that can be due to the out-crossing nature of this genus. According to observed differences for variation parameters among the three studied species, it is concluded that they have dissimilar genetic structures. The results of cluster analysis based on seed storage protein profiles in evaluated genotypes using Euclidean distance matrix and UPGMA method showed four groups. The lowest similarity coefficient was between G14 and G15 (F.arundinacea) with G6 (F.ovina). Hence, it is suggested that they evolved from a different evolutionary process and it is suggested to use them as the parents of new synthetic varieties. The observed diversity in the seed protein pattern in the three species of Festuca, can be explained by allogamy-induced-heterozygosity, species difference or population collection from various regions.

synthetic bacteria, and to have given rise to plant chloroplasts through evolution and symbiosis. The carotenoid structures and carotenogenesis pathways differ among photosynthetic bacteria, cyanobacteria, and chloroplasts, and, accordingly, carotenoids seem to change continuously. It is interesting to speculate on how these different carotenogenesis pathways have evolved and been obtained. Cyanobacteria can synthesize a variety of carotenoids. Most ordinary cyanobacteria contain β-carotene and its derivatives such as zeaxanthin, echinenone, and nostoxanthin; and also unique carotenoid glycosides, such as myxol fucoside and ketomyxol chinovoside (Takaichi and Mochimaru, 2007). These carotenoids are cyclized at one or both ends of the structure. This cyclization reaction is catalyzed by lycopene cyclase. Thus far, several types of lycopene cyclases have been confirmed in various organisms including cyanobacteria (Sugiyama et al., 2017; Takaichi, 2013; Xiong et al., 2017). Furthermore, this is the branching point of β-carotene and γ-carotene: from β-carotene, echinenone, zeaxanthin and nostoxanthin are produced; and from γ-carotene, myxol glycoside, ketomyxol glycoside and 2-hycroxymyxol glycoside are produced (Takaichi and Mochimaru, 2007). In this review, we summarize the carotenogenesis pathway, the functional enzymes as well as genes in cyanobacteria. We particularly focus on the cyclization of lycopene by distinct types of lycopene cyclases. Carotenoid biosynthesis in cyanobacteria The entire nucleotide sequence of the cyanobacteria genome was first elucidated in Synechocystis sp. PCC 6803 (Kaneko et al., 1996). Since then, the identification of carotenoids, including the chirality of hydroxyl groups and the determination of glycoside, and the genes involved in carotenogenesis, have been reported (Takaichi et al., 2001,

Next-Generation Sequencing (NGS) technologies have emerged as a powerful tool to reveal nucleotide polymorphisms in a high-throughput and cost-effective manner. However, it remains a daunting task to proficiently analyze the enormous volume of data generated from NGS and to identify length polymorphisms for molecular marker discovery. The development of insertion-deletion polymorphism (InDel) markers is in particular computationally intensive, calling for integrated high performance methods to identify InDels with high sensitivity and specificity, which would directly benefit areas from genomic studies to molecular breeding. We present here a NGS-based tool for InDel marker discovery (mInDel), a high-performance computing pipeline for the development of InDel markers between any two genotypes. The mInDel pipeline proficiently develops InDel markers by comparing shared region size using sliding alignments between assembled contigs or reference genomes. mInDel has successfully designe...

The C2H2-zinc finger proteins (ZFP) comprise a large family of transcription factors with various functions in biological processes. In maize, the function regulation of C2H2- zine finger (ZF) genes are poorly understood. We conducted an evolution analysis and functional prediction of the maize C2H2-ZF gene family. Furthermore, the ZmZFP126 gene has been cloned and sequenced for further favorable allelic variation discovery. The phylogenetic analysis of the C2H2-ZF domain indicated that the position and sequence of the C2H2-ZF domain of the poly-zinc finger gene are relatively conserved during evolution, and the C2H2-ZF domain with the same position is highly conserved. The expression analysis of the C2H2-ZF gene family in 11 tissues at different growth stages of B73 inbred lines showed that genes with multiple transcripts were endowed with more functions. The expression analysis of the C2H2-ZF gene in P1 and P2 inbred lines under drought conditions showed that the C2H2-ZF genes wer...

While the gargantuan multi-nation effort of sequencing T. aestivum gets close to completion, the annotation process for the vast number of wheat genes and proteins is in its infancy. Previous experimental studies carried out on model plant organisms such as A. thaliana and O. sativa provide a plethora of gene annotations that can be used as potential starting points for wheat gene annotations, proven that solid cross-species gene-to-gene and protein-to-protein correspondences are provided. DNA and protein sequences and corresponding annotations for T. aestivum and 9 other plant species were collected from Ensembl Plants release 22 and curated. Cliques of predicted 1-to-1 orthologs were identified and an annotation enrichment model was defined based on existing gene-GO term associations and phylogenetic relationships among wheat and 9 other plant species. A total of 13 cliques of size 10 were identified, which represent putative functionally equivalent genes and proteins in the 10 pl...

The model cyanobacterium Synechocystis sp. PCC 6803 has gained significant attention as an alternative and sustainable source for biomass, biofuels and added-value compounds. The latter category includes keto-carotenoids, which are molecules largely employed in a wide spectrum of industrial applications in the food, feed, nutraceutical, cosmetic and pharmaceutical sectors. Keto-carotenoids are not naturally synthesized by Synechocystis, at least in any significant amounts, but their accumulation can be induced by metabolic engineering of the endogenous carotenoid biosynthetic pathway. In this study, the accumulation of the keto-carotenoids astaxanthin and canthaxanthin, resulting from the constitutive or temperature-inducible expression of the CrtW and CrtZ genes from Brevundimonas, is compared. The benefits and drawbacks of the two engineering approaches are discussed.

Background: The production of glucose from cellulose requires cellulases, which are obtained from decomposing microorganisms such as fungi and bacteria. Among the cellulases, β-glucosidases convert cellobiose to glucose and have low concentration in commercial cocktails used for the production of second-generation (2G) ethanol. Genetic engineering can be used to produce recombinant β-glucosidases, and cyanobacteria may be interesting bioreactors. These photosynthetic microorganisms can be cultured using CO 2 emitted from the first-generation ethanol (1G) industry as a carbon source. In addition, vinasse, an effluent of 1G ethanol production, can be used as a source of nitrogen for cyanobacteria growth. Thus, photosynthetic bioreactors cannot only produce cellulases at a lower cost, but also reduce the environmental impact caused by residues of 1G ethanol production. Results: In the present work, we produced a strain of Synechococcus elongatus capable of expressing high levels of a heterologous β-glucosidase from a microorganism from the Amazonian soil. For this, the pET system was cloned into cyanobacteria genome. This system uses a dedicated T7 RNA polymerase for the expression of the gene of interest under the control of a nickel-inducible promoter. The results showed that the pET system functions efficiently in S. elongatus, once nickel induced T7 RNA polymerase expression which, in turn, induced expression of the gene of the microbial β-glucosidase at high levels when compared with non-induced double transgenic strain. β-glucosidase activity was more than sevenfold higher in the transformed cyanobacteria than in the wild-type strain. Conclusions: The T7 system promotes high expression levels of the cloned gene in S. elongatus, demonstrating that the arrangement in which an exclusive RNA polymerase is used for transcription of heterologous genes may contribute to high-level gene expression in cyanobacteria. This work was the first to demonstrate the use of cyanobacteria for the production of recombinant β-glucosidases. This strategy could be an alternative to reduce the release of 1G ethanol by-products such as CO 2 and vinasse, not only contributing to decrease the cost of β-glucosidase production, but also mitigating the environmental impacts of ethanol industrial plants.

Plant height (PH) and ear height (EH) are two important traits in maize (Zea mays L.), as they are closely related to lodging resistance and planting density. Our objectives were to (1) investigate single-nucleotide polymorphisms (SNPs) that are associated with PH and EH for detecting quantitative trait loci (QTL) and new gene that determines PH and EH, (2) explore the value of the QTL in maize breeding, and (3) investigate whether the "triangle heterotic group" theory is applicable for lowering PH and EH to increase yield. Seven inbred female parents were crossed with a common founder male parent Ye 107 to create a nested association mapping (NAM) population. The analysis of phenotypic data on PH and EH revealed wide variation among the parents of the NAM population. Genome-wide association study (GWAS) and high-resolution linkage mapping were conducted using the NAM population, which generated 264,694 SNPs by genotyping-by-sequencing. A total of 105 SNPs and 22 QTL were identified by GWAS and found to be significantly associated with PH and EH. A high-confidence QTL for PH, Qtl-chr1-EP, was identified on chromosome 1 via GWAS and confirmed by linkage analysis in two recombinant inbred line (RIL) populations. Results revealed that the SNP variation in the promoter region of the candidate gene Zm00001d031938, located at Qtl-chr1-EP, which encoded UDP-N-acetylglucosaminepeptide N-acetyl-glucosaminyl-transferase, might decrease PH and EH. Furthermore, the triangle heterotic pattern adopted in maize breeding programs by our team is practicable in selecting high-yield crosses based on the low ratio of EH/PH (EP).

The late Embryogenesis Abundant (LEA) protein family obtains a group of stress-induced hyper-hydrophilic proteins that accumulate in response to cellular dehydration. They are generally unstructured polypeptides without a well-defined three-dimensional structure and have been identified in a wide range of organisms from bacteria to higher plants. Herein, we made a phylogenetic and evolutionary analysis for LEA proteins in Poaceae. The full-length LEA protein sequences were acquired by performing the sequence search of sequenced hva1 against Poaceae species in the non-redundant protein database by a BlastX search tool. The sequences were aligned with the Clustal Omega tool. The MEME suite searched for conserved blocks among each LEA protein sequence. Also, the evolutionary relationship among the LEA protein sequences evaluates using the MEGA tool. The results display close sequence similarity not only into the species but also between species. The results demonstrated that LEA protein...

Transfer (T)-DNA insertions in mutants isolated from forward genetic screens are typically identified through thermal asymmetric interlaced polymerase chain reaction (TAIL-PCR), inverse PCR, or plasmid rescue. Despite the popularity and success of these methods, they have limited capabilities, particularly in situations in which the T-DNA is truncated. Here, we present a next generation sequencing (NGS)-based platform to facilitate the identification of complete and truncated T-DNA insertions. Our method enables the detection of the corresponding T-DNA insertion orientation and zygosity as well as insertion annotation. This method, called TDNAscan, was developed to be an open source software. We expect that TDNAscan will be a valuable addition to forward genetics toolkits because it provides a solution to the problem of causal gene identification, particularly genes disrupted by truncated T-DNA insertions. We present a case study in which TDNAscan was used to determine that the recessive Arabidopsis thaliana hypersensitive to latrunculin B (hlb3) mutant isolated in a forward genetic screen of T-DNA mutagenized plants encodes a class II FORMIN.

Fenugreek (Trigonella foenum-graecum L.) popularly known as “Methi” belongs to family fabaceae and subfamily papilionaceae. Gujarat Methi Variety 2 was selected for transcriptome study from the three developmental stages that were vegetative stage (20-30 DAS), reproductive stage (50-60 DAS) and maturity stage (80-90 DAS) which were sequenced using Ion S5 genome sequencing machine. Differential gene expression analysis was carried out by using CLC genomic workbench (v10.0.0). In which the data generated from transcriptome sequencing of fenugreek were mapped with the reference genome Arabidopsis thaliana, the reference genome with a length of 119,667,750 bp, total number of genes present in the reference genome were 32,833 and 49,477 transcripts. In gene expression analysis from all the three developmental stages, top 10 highly expressed genes and 10 lower regulated genes were selected. In vegetative stage, the highest expression value was 474910 and RPKM was 73070.44 for highly expre...

The introduction of mechanized agricultural practices after the Second World War and the use of productive hybrids led to a gradual disappearance of local maize varieties. However, 13 landraces are still cultivated in North-Western Italy, in the Lombardy region; those that are cultivated in mountainous areas (roughly up to 1200 m in altitude) are often characterized by the pointed shape of their seeds (i.e., “Nero Spinoso”, “Rostrato Rosso di Rovetta”, “Spinato di Gandino” and “Scagliolo di Carenno”) and the presence of pigments (i.e., “Nero Spinoso”, “Rostrato Rosso di Rovetta”). The pointed shape of the seeds is an ancient characteristic of maize-ancestors, which negatively affects the yield by not allowing optimal “filling” of the ear. This study reports work on four different Italian varieties of pointed maize in order to assess the genetic bases of the “pointed character” and to try to explain the reasons for this adaptation to the mountain environment. The data obtained by gen...

Over 3000 genomes, including numerous plant genomes, are now sequenced. However, their annotation remains problematic as illustrated by the many conserved genes with no assigned function, vague annotations such as 'kinase', or even wrong ones. Around 40% of genes of unknown function that are conserved between plants and microbes are probably metabolic enzymes or transporters; finding functions for these genes is a major challenge. Comparative genomics has correctly predicted functions for many such genes by analyzing genomic context, and gene fusions, distributions and co-expression. Comparative genomics complements genetic and biochemical approaches to dissect metabolism, continues to increase in power and decrease in cost, and has a pivotal role in modeling and engineering by helping identify functions for all metabolic genes.

Intrinsically disordered proteins (IDPs) are highly abundant in eukaryotic proteomes and involved in key biological and cellular processes. Although some resources of disordered protein predictions are available from animal and plant proteomes, those related to cereals are largely unknown. Here, we present an overview of IDPomes from Oryza sativa, Zea mays, Sorghum bicolor and Brachypodium distachyon. The work includes a comparative analysis with the model plant Arabidopsis thaliana. The data show that the intrinsic disorder content increases with the proteome size. Gene Ontology analysis reveals that IDPs in the studied species are involved mainly in regulation of cellular and metabolic processes and responses to stimulus. Our findings strongly suggest that higher plants may use common cellular and regulatory mechanisms for adaptation to various environmental constraints.

Shaping Plant Evolution Amborella trichopoda is understood to be the most basal extant flowering plant and its genome is anticipated to provide insights into the evolution of plant life on Earth (see the Perspective by Adams ). To validate and assemble the sequence, Chamala et al. (p. 1516 ) combined fluorescent in situ hybridization (FISH), genomic mapping, and next-generation sequencing. The Amborella Genome Project (p. 10.1126/science.1241089 ) was able to infer that a whole-genome duplication event preceded the evolution of this ancestral angiosperm, and Rice et al. (p. 1468 ) found that numerous genes in the mitochondrion were acquired by horizontal gene transfer from other plants, including almost four entire mitochondrial genomes from mosses and algae.

We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. The results demonstrate that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres revealed additional variation in major cytological landmarks. We show that combining structural variation with single-nucleotide polymorphisms can improve the power of quantitative mapping studies. We also document variation at the level of DNA methylation and demonstrate that unmethylated regions are enriched for cis-regulatory elements that contribute to phenotypic variation.

P2- type calcium ATPases (ACAs-auto inhibited calcium ATPases and ECAs-endoplasmic reticulum calcium ATPases) belong to the P- type ATPase family of active membrane transporters and are significantly involved in maintaining accurate levels of Ca2+, Mn2+ and Zn2+ in the cytosol as well as playing a very important role in stress signaling, stomatal opening and closing and pollen tube growth. Here we report the identification and possible role of some of these ATPases from wheat. In this study, ACA and ECA sequences of six species (belonging to Poaceae) were retrieved from different databases and a phylogenetic tree was constructed. A high degree of evolutionary relatedness was observed among P2 sequences characterized in this study. Members of the respective groups from different plant species were observed to fall under the same clade. This pattern highlights the common ancestry of P2- type calcium ATPases. Furthermore, qRT-PCR was used to analyse the expression of selected ACAs and ...

In southwest China, some maize landraces have long been isolated geographically, and have phenotypes that differ from those of widely grown cultivars. These landraces may harbor rich genetic variation responsible for those phenotypes. Four-row Wax is one such landrace, with four rows of kernels on the cob. We resequenced the genome of Four-row Wax, obtaining 50.46 Gb sequence at 21.87× coverage, then identified and characterized 3,252,194 SNPs, 213,181 short InDels (1-5 bp) and 39,631 structural variations (greater than 5 bp). Of those, 312,511 (9.6%) SNPs were novel compared to the most detailed haplotype map (HapMap) SNP database of maize. Characterization of variations in reported kernel row number (KRN) related genes and KRN QTL regions revealed potential causal mutations in fea2, td1, kn1, and te1. Genome-wide comparisons revealed abundant genetic variations in Four-row Wax, which may be associated with environmental adaptation. The sequence and SNP variations described here enrich genetic resources of maize, and provide guidance into study of seed numbers for crop yield improvement.

Despite advances in sequencing, the goal of obtaining a comprehensive view of genetic variation in populations is still far from reached. We sequenced 180 lines of A. thaliana from Sweden to obtain as complete a picture as possible of variation in a single region. Whereas simple polymorphisms in the unique portion of the genome are readily identified, other polymorphisms are not. The massive variation in genome size identified by flow cytometry seems largely to be due to 45S rDNA copy number variation, with lines from northern Sweden having particularly large numbers of copies. Strong selection is evident in the form of long-range linkage disequilibrium (LD), as well as in LD between nearby compensatory mutations. Many footprints of selective sweeps were found in lines from northern Sweden, and a massive global sweep was shown to have involved a 700-kb transposition.

Shaping Plant Evolution Amborella trichopoda is understood to be the most basal extant flowering plant and its genome is anticipated to provide insights into the evolution of plant life on Earth (see the Perspective by Adams ). To validate and assemble the sequence, Chamala et al. (p. 1516 ) combined fluorescent in situ hybridization (FISH), genomic mapping, and next-generation sequencing. The Amborella Genome Project (p. 10.1126/science.1241089 ) was able to infer that a whole-genome duplication event preceded the evolution of this ancestral angiosperm, and Rice et al. (p. 1468 ) found that numerous genes in the mitochondrion were acquired by horizontal gene transfer from other plants, including almost four entire mitochondrial genomes from mosses and algae.

Coffee, tea, and chocolate converge Caffeine has evolved multiple times among plant species, but no one knows whether these events involved similar genes. Denoeud et al. sequenced the Coffea canephora (coffee) genome and identified a conserved gene order (see the Perspective by Zamir). Although this species underwent fewer genome duplications than related species, the relevant caffeine genes experienced tandem duplications that expanded their numbers within this species. Scientists have seen similar but independent expansions in distantly related species of tea and cacao, suggesting that caffeine might have played an adaptive role in coffee evolution. Science , this issue p. 1181 ; see also p. 1124

Whereas breeders have exploited diversity in maize for yield improvements, there has been limited progress in using beneficial alleles in undomesticated varieties. Characterizing standing variation in this complex genome has been challenging, with only a small fraction of it described to date. Using a population genetics scoring model, we identified 55 million SNPs in 103 lines across pre-domestication and domesticated Zea mays varieties, including a representative from the sister genus Tripsacum. We find that structural variations are ...

Domestication and plant breeding are ongoing 10,000-year-old evolutionary experiments that have radically altered wild species to meet human needs. Maize has undergone a particularly striking transformation. Researchers have sought for decades to identify the genes underlying maize evolution 1, 2, but these efforts have been limited in scope. Here, we report a comprehensive assessment of the evolution of modern maize based on the genome-wide resequencing of 75 wild, landrace and improved maize lines 3. We find ...

Whereas breeders have exploited diversity in maize for yield improvements, there has been limited progress in using beneficial alleles in undomesticated varieties. Characterizing standing variation in this complex genome has been challenging, with only a small fraction of it described to date. Using a population genetics scoring model, we identified 55 million SNPs in 103 lines across pre-domestication and domesticated Zea mays varieties, including a representative from the sister genus Tripsacum. We find that structural variations are ...

Shaping Plant Evolution Amborella trichopoda is understood to be the most basal extant flowering plant and its genome is anticipated to provide insights into the evolution of plant life on Earth (see the Perspective by Adams ). To validate and assemble the sequence, Chamala et al. (p. 1516 ) combined fluorescent in situ hybridization (FISH), genomic mapping, and next-generation sequencing. The Amborella Genome Project (p. 10.1126/science.1241089 ) was able to infer that a whole-genome duplication event preceded the evolution of this ancestral angiosperm, and Rice et al. (p. 1468 ) found that numerous genes in the mitochondrion were acquired by horizontal gene transfer from other plants, including almost four entire mitochondrial genomes from mosses and algae.

Introduction: Darwin famously characterized the rapid rise and early diversifi cation of fl owering plants (angiosperms) in the fossil record as an "abominable mystery." Identifying genomic changes that accompanied the origin of angiosperms is key to unraveling the molecular basis of biological innovations that contributed to their geologically near-instantaneous rise to ecological dominance. Methods: We provide a draft genome for Amborella trichopoda, the single living representative of the sister lineage to all other extant fl owering plants and use phylogenomic and comparative genomic analyses to elucidate ancestral gene content and genome structure in the most recent common ancestor of all living angiosperms. Results: We reveal that an ancient genome duplication predated angiosperm diversifi cation. However, unlike all other sequenced angiosperm genomes, the Amborella genome shows no evidence of more recent, lineage-specifi c genome duplications, making Amborella particularly well suited to help interpret genomic changes after polyploidy in other angiosperms. The remarkable conservation of gene order (synteny) among the genomes of Amborella and other angiosperms has enabled reconstruction of the ancestral gene arrangement in eudicots (~75% of all angiosperms). An ancestral angiosperm gene set was inferred to contain at least 14,000 protein-coding genes; subsequent changes in gene content and genome structure across disparate fl owering plant lineages are associated with the evolution of important crops and model species. Relative to nonangiosperm seed plants, 1179 gene lineages fi rst appeared in association with the origin of the angiosperms. These include genes important in fl owering, wood formation, and responses to environmental stress. Unlike other angiosperms, the Amborella genome lacks evidence for recent transposon insertions while retaining ancient and divergent transposons. The genome harbors an abundance of atypical lineage-specifi c 24-nucleotide microRNAs, with at least 27 regulatory microRNA families inferred to have been present in the ancestral angiosperm. Population genomic analysis of 12 individuals from across the small native range of Amborella in New Caledonia reveals geographic structure with conservation implications, as well as both a recent genetic bottleneck and high levels of genome diversity. Discussion: The Amborella genome is a pivotal reference for understanding genome and gene family evolution throughout angiosperm history. Genome structure and phylogenomic analyses indicate that the ancestral angiosperm was a polyploid with a large constellation of both novel and ancient genes that survived to play key roles in angiosperm biology. Tables S1 to S46 Additional Acknowledgment References RELATED ITEMS IN SCIENCE K. Adams, Genomic clues to the ancestral fl owering Plant.

Mechanosensitive ion channels are pore-forming transmembrane proteins that allow ions to move down their electrochemical gradient in response to mechanical stimuli. They participate in many plant developmental processes including the maintenance of plastid shape, pollen tube growth, etc. Herein, a total of 11, 10, 6, 30, 9, and 8 MSL genes were identified in Aegilops tauschii, Hordeum vulgare, Sorghum bicolor, Triticum aestivum, Triticum urartu, and Zea mays, respectively. These genes were located on various chromosomes of their respective cereal, while MSLs of T. urartu were found on scaffolds. The phylogenetic analysis, subcellular localization, and sequence homology suggested clustering of MSLs into two classes. These genes consisted of cis-regulatory elements related to growth and development, responsive to light, hormone, and stress. Differential expression of various MSL genes in tissue developmental stages and stress conditions revealed their precise role in development and s...

Pineapple (Ananas comosus (L.) Merr.) is the most economically valuable crop possessing crassulacean acid metabolism (CAM), a photosynthetic carbon assimilation pathway with high water-use efficiency, and the second most important tropical fruit. We sequenced the genomes of pineapple varieties F153 and MD2 and a wild pineapple relative, Ananas bracteatus accession CB5. The pineapple genome has one fewer ancient whole-genome duplication event than sequenced grass genomes and a conserved karyotype with seven chromosomes from before the ρ duplication event. The pineapple lineage has transitioned from C3 photosynthesis to CAM, with CAM-related genes exhibiting a diel expression pattern in photosynthetic tissues. CAM pathway genes were enriched with cis-regulatory elements associated with the regulation of circadian clock genes, providing the first cis-regulatory link between CAM and circadian clock regulation. Pineapple CAM photosynthesis evolved by the reconfiguration of pathways in C3...

In Mexico's territory, the center of origin and domestication of maize (Zea mays), there is a large phenotypic diversity of this crop. This diversity has been classified into "landraces." Previous studies have reported that genomic variation in Mexican maize is better explained by environmental factors, particularly those related with altitude, than by landrace. Still, landraces are extensively used by agronomists, who recognize them as stable and discriminatory categories for the classification of samples. In order to investigate the genomic foundation of maize landraces, we analyzed genomic data (35,909 SNPs from Illumina MaizeSNP50 BeadChip) obtained from 50 samples representing five maize landraces (Comiteco, Conejo, Tehua, Zapalote Grande, and Zapalote Chico), and searched for markers suitable for landrace assignment. Landrace clusters could not be identified taking all the genomic information, but they become manifest taking only a subset of SNPs with high FST am...

The late Embryogenesis Abundant (LEA) protein family obtains a group of stress-induced hyper-hydrophilic proteins that accumulate in response to cellular dehydration. They are generally unstructured polypeptides without a well-defined three-dimensional structure and have been identified in a wide range of organisms from bacteria to higher plants. Herein, we made a phylogenetic and evolutionary analysis for LEA proteins in Poaceae. The full-length LEA protein sequences were acquired by performing the sequence search of sequenced hva1 against Poaceae species in the non-redundant protein database by a BlastX search tool. The sequences were aligned with the Clustal Omega tool. The MEME suite searched for conserved blocks among each LEA protein sequence. Also, the evolutionary relationship among the LEA protein sequences evaluates using the MEGA tool. The results display close sequence similarity not only into the species but also between species. The results demonstrated that LEA protein...

Mechanisms involved in the de-acclimation of herbaceous plants caused by warm periods during winter are poorly understood. This study identifies the genes associated with this mechanism in winter barley. Seedlings of eight accessions (four tolerant and four susceptible to de-acclimation cultivars and advanced breeding lines) were cold acclimated for three weeks and de-acclimated at 12 °C/5 °C (day/night) for one week. We performed differential expression analysis using RNA sequencing. In addition, reverse-transcription quantitative real-time PCR and enzyme activity analyses were used to investigate changes in the expression of selected genes. The number of transcripts with accumulation level changed in opposite directions during acclimation and de-acclimation was much lower than the number of transcripts with level changed exclusively during one of these processes. The de-acclimation-susceptible accessions showed changes in the expression of a higher number of functionally diverse g...