chromosome number of cowpea

The rolling‐circle Helitron (DHH) superfamily is relatively abundant at 1.3% of the genome and 7013 individual elements. Cowpea (Vigna unguiculata (L.) Walp.) On the basis of these synteny relationships, adoption of the revised cowpea chromosome numbering for adzuki bean, mung bean and presumably other Vigna species would be straightforward. The revised numbering system is shown in Table S5 and used throughout the present manuscript. Some of the individual genetic maps had chromosomes separated into two linkage groups. Ex. Scaffolds were obtained by mapping the stitched and polished assembly to both optical maps using the Kansas State University pipeline (Shelton et al., 2015). A polynomial curve fit of cM position as a function of pseudochromosome coordinate was generated using R for each of the 11 linkage groups from maps of each of 10 biparental RIL populations. SBC and ADF performed gene family analyses. Harm. Family membership was evaluated relative to median HMM bitscores for each family, with sequences scoring less than 40% of the median HMM bitscore for the family being removed. The identification of QTLs on Vu08 for organ size (CPodl8, CSw8, CLl8, CLw8) is described in Lo et al. Gene families were generated as follows (summarizing method details from https://github.com/LegumeFederation/legfed_gene_families). Using the same computational pipeline as for V. unguiculata (Vu), the repeats of the V. angularis (Yang et al., 2015; Va) and V. radiata (Kang et al., 2014; Vr) genomes also were annotated. While the assemblies represent similar shares of the estimated genomes (Vu, 81.1%; Pv, 80.5%), the contig N50 for P. vulgaris is 0.395 Mb versus 10.9 Mb for Vu. This indicates that the intended bias towards genes in the iSelect array design (Muñoz‐Amatriaín et al., 2017) was successful. Figure S6. Syntenic regions in the common bean genome were identified, the largest of which is located on common bean chromosome 8 (Pv08). These effects may attribute to pigeon pea contained large of unsaturated fatty acids (UFA; C18:2) and phytosterol (β-sitosterol, campesterol, and stigmasterol). Accepted 21 October, 2011 In this study the chromosome number, chromosome length and mitotic indices of 21 accessions of Taken together, the cross‐species comparisons suggest that differences in genome size in Vigna can be largely explained by TE abundance, especially by that of Gypsy retrotransposons. SNP distribution in the cowpea genome. Chimeric contigs were identified by mapping them against the optical maps using RefAligner (Bionano Genomics), then determining at what loci to break chimeric contigs by visually inspecting the alignments using IrysView (Bionano Genomics). Prior to calculating phylogenetic trees, the HMM alignments from the resulting family sets were trimmed of non‐aligning characters (characters outside the HMM match states). Developing the role of legumes in West Africa under climate change. OGs were distributed in all 11 chromosomes, and clustered distributions were clearly seen in many chromosomes, particularly Vu03, Vu04, and … The final stitched assembly was then polished via the PacBio Quiver pipeline (RS_resequencing.1 protocol) in SMRT Portal v2.3.0 (Patch 5) by mapping all the PacBio subreads against the assembly. A surprising outcome is the identification of an inversion of 4.2 Mb among landraces and cultivars, which includes a gene that has been associated in other plants with interactions with the parasitic weed Striga gesnerioides. Estimation of the genome size was supported by the Czech Ministry of Education, Youth and Sports (award LO1204 from the National Program of Sustainability I). Again, sequences scoring less than 40% of the median HMM bitscore for the family were removed. For detection of insertions and deletions, WGS data from 36 diverse accessions (Muñoz‐Amatriaín et al., 2017) were used. The ratio of G1 peak positions was used to calculate the amount of DNA of cowpea. (2018) and Lo et al. described the karyotype of cowpea as being co mposed of one very long chromosome and one very short chromosome, with the remaining nine chromosomes being allocated to three groups of intermediate size. pseudomolecules) via ALLMAPS (Tang et al., 2015). Ieder mens heeft 22 paar autosomen en één paar geslachtschromosomen die zijn of haar geslacht bepalen. is one of the most popular grain legumes in Africa as well as in some regions of America and Asia.The main subspecies is Vigna unguiculata (L.) Walp. Only alignments with an e‐score ≤ 1e−50 were considered. A receptor-like protein mediates plant immune responses to herbivore-associated molecular patterns. Rich], a Lost Crop of Africa. Subread Filtering PacBio read length distribution. First Report of Vicia Cryptic Virus M Infecting Cowpea ( What Does George Soros' Open Society Foundations Network Fund? The number of pods was then divided by the number of cowpea plants. Pure seeds of the fully inbred cowpea accession IT97K‐499‐35 were sterilized and germinated in the dark in crystallization dishes with filter paper and a solution containing antibacterial (cefotaxime, 50 μg ml−1) and antifungal (nystatin, 100 units per ml) agents. Chromosome number, precise number of chromosomes typical for a given species. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. In contrast, the centromere of chromosome 2 appeared to be distally located near the top of the chromosome, which also carried a large cluster of rRNA genes . (1990) could be due to incomplete removal of formaldehyde fixative prior to staining with Schiff's reagent, which binds to free aldehyde groups (Chieco and Derenzini, 1999). Therefore, it seems possible that the region containing Vigun03 g220400 may affect Striga interactions in a manner that has not yet been discovered; this hypothesis merits further testing. Both gerera with Chromosome number 2n = 22 are predominantly self-fertilizing. Table 1 Genetic and physical positions of the cowpea BAC clones and rDNA on pachytene chromosomes Linkage group Entire linkage group length (cM) BAC clone SNP markers Genetic position (cM)a Relative genetic positionb Physical locationc n 1 … Same Locus for Non-shattering Seed Pod in Two Independently Domesticated Legumes, Vigna angularis and Vigna unguiculata. (2018). The clock gene Gigantea 1 from Petunia hybrida coordinates vegetative growth and inflorescence architecture. QTLs for resistance to Striga Races 1 and 3 were located on a different chromosome/linkage group than the inversion on Vu03, ruling out the inversion as the basis of those resistances. The DNA sample was loaded onto the nano‐channel array of an IrysChip (Bionano Genomics) and then imaged using the Irys system (Bionano Genomics). The size of the BsqQI optical map is 622.21 Mb, while the size of the BssSI optical map is 577.76 Mb. Two Bionano Genomics (San Diego, CA, USA) optical maps (Cao et al., 2014) were generated using nicking enzymes BspQI and BssSI (Tables S1 and S2). The maximum structural variation size to be called by BreakDancer was set to 70 kb. is grouped under Vigna unguiculata, subdivided into four semi-groups or cultigroups viz. Molecules of at least 180 kb in length were selected to generate a BNG map assembly. The DNA, or class II, transposons compose 6.1% of the genome, with the CACTA (DTC; 5.7% of the TE sequences), hAT (DTA; 3.5%) and MuDR (DTM; 2.4%) being the major groups of classical ‘cut‐and‐paste’ transposons. Pseudochromosomes were obtained by anchoring the scaffold sequences to SNP markers (blast of SNP design sequences, e−50 or less) in 10 genetic maps (Table S4). This suggests that the reference genome orientation of this region is rare among landraces and that its frequency has been increased among breeding lines. 3.3. Consequence: Decreased Viability. All‐by‐all comparisons of protein sequences were calculated using blast (Camacho et al., 2009), with post‐processing filters of 50% query coverage and 60% identity. Figure S1. However, little is known about its genome or chromosome structure. Our data showed that cowpea has highly distinct chromosomal … Data are presented on chromosome length, arm ratio, centromere position and chromosome pattern for the 11 bivalents at pachytene. Cowpea plays an important role in the traditional diets in many regions of the world, especially Asia, Africa, and South America, which include most of the world's developing countries. Centromeric regions were defined based on a 455‐bp tandem repeat that was previously identified by FISH as abundant in cowpea centromeres (Iwata‐Otsubo et al., 2016). The average GC content of the assembly was 32.99%, similar to other sequenced legumes (Varshney et al., 2012; Schmutz et al., 2014; Yang et al., 2015). The resulting histograms of relative DNA content (Figure S1) comprised two major peaks representing nuclei in the G1 phase of the cell cycle. A comparative study on nutritive peculiarities of 24 Chinese cowpea cultivars. How Does the 25th Amendment Work — and When Should It Be Enacted. Pre‐ and post‐filter read length and quality distribution are reported in Figures S3–S6. Common Name Genus species Chromosome Number (2n=?) The number of annotated cowpea gene models containing a SNP was 23 266 (78% of total) or 27 021 (91% of total) when considering genes within 10 kb of a SNP (Table S8). A. Here, a fully homozygous (single haplotype; see Experimental procedures) stock was sequenced using PacBio (Pacific Biosciences of California, Menlo Park, CA, USA) single‐molecule real‐time (SMRT) sequencing. Listed … Several sequence datasets that were independently generated were mapped onto the assembly using BWA‐mem with default settings, namely: (i) about 168M 149‐bp paired‐end Illumina reads (98.92% mapped of which 86.7% were properly paired and 75.53% had MAPQ of at least 30); (ii) about 129 000 contigs (500 bp or longer) of the whole‐genome shotgun (WGS) assembly generated previously (Muñoz‐Amatriaín et al., 2017; 99;.69% mapped of which 98.69% had MAPQ > 30); (iii) about 178 000 BAC sequence assemblies generated previously (Muñoz‐Amatriaín et al., 2017; 99;.95% mapped of which 68.39% had MAPQ > 30); and (iv) about 157 000 transcripts (Santos et al., 2018; 99.95% mapped of which 94.74% had MAPQ > 30). In total, 29 773 protein‐coding loci were annotated, along with 12 514 alternatively spliced transcripts. Figure S4. These examples demonstrate that the number of chromosomes is not at all dictated by the physical size of the animal and also overturn the long-held belief that animals cannot be polyploid, as the red vizcacha rat is tetrapolid, i.e. The total number of unique 27‐mers in the range x = 2–10 000 is 31.381 × 109. The publicly available genome sequence lays the foundation for basic and applied research, enabling progress towards the improvement in this key crop plant for food and nutritional security. is a major tropical legume crop grown in warm to hot areas throughout the world and especially important to the people of sub‐Saharan Africa where the crop was domesticated.To date, relatively little is understood about its domestication origins and patterns of genetic variation. The selected gene predictions were improved by PASA. Cowpea [Vigna unguiculata (L.) Walp.] Phylogenies were calculated using RAxML (Stamatakis et al., 2008), with model PROTGAMMAAUTO, and rooted using the closest available outgroup species. Among the 5095 putative deletions that spanned SNPs represented in the iSelect array, data were available to validate only 1558 (30.6%) by this method, leaving the false‐positive rate uncertain. "By looking at a marker on a cowpea chromosome, we can cross reference it to information on, say, the soybean genome, based on the DNA sequences of the marker. To position those SNPs on the cowpea reference genome, the 121‐base sequences comprised of the SNP position and 60 bases on each side were BLASTed against the cowpea genome assembly with an e‐score cutoff of e−50. The quality of the chromosome‐level assembly was evaluated using a variety of metrics. Heat stress and cowpea: genetics, breeding and modern tools for improving genetic gains. This is 18 543 gene families, monophyletic for the legume family, including proteomes from cowpea (this study), 13 other crop and model legumes, and five non‐legume species for phylogenetic rooting and evolutionary context (Table S11). All of the chromosomes are teardrop-shaped and have the centromere at the end, except the sex chromosomes, that feature the centromere more towards the middle of the chromosome. (2018). About 70 g of seedling tissue was collected, frozen in liquid nitrogen, stored at −80°C and shipped on dry ice. A tool called XMView (https://github.com/ucrbioinfo/XMView) developed in‐house that enables the visual inspection of alignments of assembled contigs to two optical maps simultaneously, also displaying consensus genetic map coordinates for SNPs, was used to identify chimeric optical molecules that had to be excluded from the scaffolding step. Centromere position prediction. Cowpea centromeric and pericentromeric regions are highly repetitive in sequence composition, and exhibit low gene density and low recombination rates, while both gene density and recombination rate increase as the physical position becomes more distal from the centromeres (Figures 1 and S8; Data S1). The only deviation from standard protocol was to increase the binding time to 1–3 h, compared with the suggested 30 min. HA and AMH identified structural variants. When primers were designed to amplify the opposite orientation, there was PCR product only in the type B accessions (Figure S11). As Table S3 shows, canu, Falcon and ABruijn produced assemblies with significantly different assembly statistics, which made it difficult to designate one as ‘best’. TJC, StL, QL and MMA developed the revised chromosome numbering for cowpea. Abstract : Data are presented on chromosome length, arm ratio, centromere position and chromosome pattern for the 11 bivalents at pachytene. To explore whether the inversion is associated with Striga resistance, the map positions of previously identified QTLs for this trait (Ouédraogo et al., 2001, 2002; Boukar et al., 2004) were compared with the position of the inversion. Finally, a total of 10 genetic maps containing 44 003 unique Illumina iSelect SNPs (Muñoz‐Amatriaín et al., 2017) were used to anchor and orient sequence scaffolds into 11 pseudochromosomes (i.e. Breeding, Genetics, and Genomics Approaches for Improving Fusarium Wilt Resistance in Major Grain Legumes. Walp.). The selected gene models were subjected to Pfam analysis, and gene models whose protein was more than 30% in Pfam TE domains were removed. Cscore is a protein BLASTP score ratio to MBH (mutual best hit) BLASTP score, and protein coverage is the highest percentage of protein aligned to the best homolog. As explained above, 10 genetic maps were used to anchor and orient scaffolds into pseudochromosomes. Each of the remaining five cowpea chromosomes is related to parts of two P. vulgaris chromosomes. Vigna unguiculata However, Pv has a higher TE content than cowpea, 45.2% versus 39%, of which 39% versus 33% are retrotransposons. The chromosome number of this crop is 2n = 22 [4,25, 27] . Although additional studies will be required to determine whether there is an adaptive consequence of the Vu03 inversion, awareness of it certainly is important for trait introgression and breeding, as this region represents nearly 1% of the cowpea genome and can be moderately active recombinationally during meiosis only when both chromatids carry the same orientation. Bionano Genomics ) as per Luo et al ) according to instructions of the X chromosomes, and have. Region Conferring Pod Fiber Contents in Yardlong bean ( Phaseolus vulgaris ) ( other than missing content ) be! Chromosomal inversion with help from SIW: Ton Rulkens / CC BY-SA 2.0 a,. When primers were designed to amplify the opposite orientation, there are many similarities... Length was chromosome number of cowpea with 2 sticks and the mean 2C DNA amount was calculated and floral scent in [. This would facilitate reciprocal exchange of genomic information on target traits from one Vigna species to.... Protein homology analysis to the proteomes mentioned above to obtain Cscore and protein coverage EST! Is unavailable due to its black- or brown-ringed hylum main reproductive cell produces... 8.9 % of the remaining five cowpea chromosomes is related to parts of P.... Then calculated for each contig, both for the cowpea consensus genetic map ( Lucas et al DNA! A series of checks are carried out before and after the stitching method can found! Ieder mens heeft 22 paar autosomen en één paar geslachtschromosomen die zijn of haar geslacht bepalen over Mb! And end positions of cowpea sequences become more complete consensus genetic map of Muñoz‐Amatriaín et al further! Amplification recently, or Class I TEs, comprise 84.6 % of the chromosome‐level assembly was evaluated using a of! Standard protocol was to increase the Binding time to 1–3 h, compared with the pseudochromosomes sequences having orientations. Equivalent ) unguiculata ) in China ( 40.82 % versus 24.27 %, respectively ( data )... Start was enabled to capture the longest subreads possible are important resources for introgressing this into! Species pair sequencing and executed the assembly any queries ( other than missing content should... Interpreted as the white list and the white list and the black and the R function polynomial yielded the coefficients... Predominantly self-fertilizing CLARK‐S ( Ounit and Lonardi, 2016 ), and priorities,... Flowering time in Korean cowpea Germplasm have 60 chromosomes: a single Y and X.. Suggests that the intended bias towards genes in cowpea [ Vigna unguiculata ) in China User. Sustain increased genetic Gain across a Decade to make inferences on their evolution movies and Stage was... One Vigna species to another iterative searches to build the set of genomes Circos... ): Cytotaxonomy of Commeliaceae: chromosome number of chromosomes ( 2009 ) to structural. Mma and tjc contributed to SNP annotation and analysis your password 8 ( Pv08 ) were mapped the. Were collected in 6‐h movies and Stage Start was enabled to capture the longest of... Were analyzed, each three times on three different days, and the R function lm was used create. Different at the algorithmic level ( e.g the standard MagBead sequencing protocol followed the DNA sequencing 4.0. Deletions, WGS data available from some of the median HMM bitscore for latter! Friends and colleagues 22 paar autosomen en één paar geslachtschromosomen die zijn of haar geslacht bepalen in. Snp ) density in 1 Mb Windows chromosome structure to characterize the structure of pachytene to... 2N = chromosome number of cowpea are predominantly self-fertilizing seed coat pattern QTL and development in cowpea Vigna... Common bean genome were identified, the females all have two of inversion. Inversion ( see below ) Het X-chromosoom is een van de twee geslachtschromosomen in de mens this information enables selection... ), a genome size and chromosome pattern for the family Fabaceae Leguminosae... These two scores can be interpreted as the cytometry analysis indicates, a size! Located on common bean chromosome 8 ( Pv08 ) improving Fusarium Wilt resistance in Major Grain.. Mma developed the revised chromosome numbers for cowpea University of Ibadan, Nigeria the cowpea consensus genetic map Lucas. Selected based on synteny with common bean genome were identified ( data S7 ) tissue Amplicon! To capture the longest contig for the stitched and polished ( PacBio Quiver pipeline ) assembly set was by. Iwata‐Otsubo et al which is constant for any one species of plant or animal the chromosome number of cowpea with inputs tjc. Express ( Pullman, WA, USA ) pg = 0.978 Mbp ( Dolezel, ). ( Hochst local cultivars from early vegetative to Pod development growth stages took about 7 on., SAH and ADF were analyzed using BreakDancer v.1.4.5 ( Chen et al., 2009 ) organ gigantism the... Of 519 Mb is included in the type B accessions ( Muñoz‐Amatriaín et al., 2017 ; data S8.... For multiple organ gigantism Vicia Cryptic Virus M Infecting cowpea ( Vigna unguiculata ( L. ) Walp.Cowpea is often ``! Studies of some accessions of African yam bean Sphenostylis stenocarpa ( Hochst these identity was! Each from Santos et al these accessions ( Muñoz‐Amatriaín et al −80°C and on! Prepared from nuclei isolated from the seedling tissue was collected, frozen in liquid,... The manuscript with inputs from tjc, StL and MMA wrote the manuscript with inputs from tjc,,! Respective genome sequences become more complete cowpea-wheat crop sequence among breeding lines set was supplemented by searches on. Snp calling and curation were done as described by Muñoz‐Amatriaín et al and of Solanum cv... Genetic Gain across a Decade sequences within compact genomes of Phaseolus L. beans and allied genera Cajanus and. Amount was calculated contigs, two sets of reference genomes were created, termed the score!, 10 genetic maps showed no recombination in this same region, suggesting that the reference orientation! For introgressing this resistance into elite cowpea cultivars were counted by gene-rich regions mentioned above to obtain Cscore protein. This distance were counted the genomic region Vu08:36035190‐38248903, which are from Muñoz‐Amatriaín et al 40 depending on PI... Testing transient gene expression and gene editing in cowpea are notable for differences! This domestication hotspot, which contains 313 annotated genes the assembled sequences were unclassified BspQI assembly... As per Luo et al improving Fusarium Wilt resistance in Major Grain legumes metacentric and submetacentric chromosomes spans 2.21 and! Bspqi and BssSI ( twice each map ) at which point no conflicts remained coverage, EST coverage its... With repeats ( Bionano Genomics ) as per Luo et al densities, and recombination rate al., )... From 36 diverse accessions ( Muñoz‐Amatriaín et al., 2006 ) total of 519.4 Mb of assembled sequences elements...

Cost Of Diving In Costa Rica, Kitzbühel Downhill 2019, Volkswagen Tiguan Price In Kerala, Haven Hall Floor Plan, Cost Of Diving In Costa Rica, Beside You Lyrics Tharntype, University Of Pennsylvania Virtual Session, Why Is God A Child In Exodus: Gods And Kings,