chromosome number of cowpea

Cowpea is a diploid member of the Fabaceae family with a chromosome number 2n = 22 and a previously estimated genome size of 613 Mb (Arumuganathan and Earle, 1991). Almost all (99.83%) of the 957 710 discovered single nucleotide polymorphisms (SNPs; hereinafter referred as the ‘1M list’) were positioned in the reference sequence, including 49 697 SNPs that can be assayed using the Illumina iSelect Consortium Array (Muñoz‐Amatriaín et al., 2017; Data S2). "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. Helitrons contributed 10% (versus Vr) or 11% (versus Va) to the expansion of the cowpea genome, and increased in genome share by an order of magnitude. The differential abundance of Gypsy elements in cowpea amounts to 58 and 56% of the total contribution of TEs to its genome size difference with mung bean and adzuki bean, respectively. Loci were determined by transcript assembly alignments and/or EXONERATE alignments of proteins from Arabidopsis, common bean, soybean, Medicago, poplar, rice, grape and Swiss‐Prot proteomes to repeat‐soft‐masked cowpea genome using RepeatMasker (Smit et al., 2017) with up to 2 kb extension on both ends unless extending into another locus on the same strand. Comparing Vu with Vr, 94% of the 56 Mbp size difference can be explained by the differential abundance of TEs, and 57% by the differential abundance of superfamily Gypsy retrotransposons alone (Table S9). Pre‐filter PacBio read length distribution. The repeat library consisted of de novo repeats identified by RepeatModeler (Smit et al., 2008) and Fabaceae repeats in RepBase. Regions containing this sequence span over 20.18 Mb (3.9% of the assembled genome; Table S7). Figure S4. 200pp. Cowpea [Vigna unguiculata (L.) Walp.] Figure S6. Its genome shares a high degree of collinearity with other warm‐season legumes (Phaseoleae tribe), including common bean (Phaseolus vulgaris L.; Vasconcelos et al., 2015; Muñoz‐Amatriaín et al., 2017). The remaining three genetic maps were generated as part of this study after genotyping three additional RIL populations with the Cowpea iSelect Consortium Array (Muñoz‐Amatriaín et al., 2017). is one of the most important food and nutritional security crops, providing the main source of protein to millions of people in developing countries. The output alignments between genomes were visualized using Circos v0.69‐3 (Krzywinski et al., 2009; Figure 3). Ex. Each assembled contig was BLASTed against the ‘white’ genome and the ‘black’ genomes, and all high‐quality alignments (e‐score < 1e−47 corresponding to a bit score of at least 200, and covering at least 10% of the read length) were recorded. The original PacBio reads were also mapped onto the assembly using BLASR using default settings: 5.29 M long reads mapped for a total of about 46 × 109 bp; 88.68% of the bases of the long reads were present in the 519 Mbp assembly. pseudomolecules) via ALLMAPS (Tang et al., 2015). The assembled genome was annotated using de novo gene prediction and transcript evidence based on cowpea ESTs (Muchero et al., 2009) and RNA‐seq data from leaf, stem, root, flower and seed tissue (Yao et al., 2016; Santos et al., 2018), and protein sequences of Arabidopsis, common bean, soybean, Medicago, poplar, rice and grape (see Experimental procedures). The SNP markers associated with those QTLs span the genomic region Vu08:36035190‐38248903, which contains 313 annotated genes. 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These two scores can be interpreted as the weighted coverage of a contig by statistically significant alignments from the respective set of genomes. Chromomeres were not distributed uniformly along the arms. Its genome shares a high degree of collinearity with other warm‐season legumes (Phaseoleae tribe), including common bean ( Phaseolus vulgaris L.; Vasconcelos et al ., 2015 ; Muñoz‐Amatriaín et al ., 2017 ). In general, SNP density was lowest near centromeric regions (Figures 1 and S9). subsp. Our data showed that cowpea has highly distinct … JD and JV estimated the genome size. For the latter, the sequence assembly of the California accession was used to design primers. The cutoff limit was set to 15–50 kb to select SMRTbell library molecules with an average size of 20 kb or larger. Clearly, there are many structural similarities but also some differences between common bean and cowpea chromosomes. All of these families occur in large genomic arrays, which can expand or contract, likely through slipped‐strand mispairing of paralogous genes (Levinson and Gutman, 1987; Cannon et al., 2004; Li et al., 2016). The resulting histograms of relative DNA content (Figure S1) comprised two major peaks representing nuclei in the G1 phase of the cell cycle. Cowpea (Vigna unguiculata [L.] Walp.) PCR amplifications of the breakpoint regions were performed to further validate the Vu03 inversion. 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. Extensive synteny has been previously observed between cowpea and common bean (Muñoz‐Amatriaín et al., 2017), which facilitates a revised chromosome numbering system for cowpea based on synteny with common bean. What Are the Steps of Presidential Impeachment? Rich], a Lost Crop of Africa. To classify the repeats, an identity of at least 8 and minimal hit length 80 bp were required. (2017), raw Illumina reads from 37 diverse cowpea accessions are available under SRA accession SRP077082. 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). Yielded the polynomial coefficients all have two of the 110 selected polynomials to represent the of., including distance to gene and repeat densities, and the BNG BssSI map.... Fiber Contents in Yardlong bean ( Vigna mungo ) genome, MMA and tjc contributed to the proteomes mentioned to. Here was used to identify structural variants African cowpea Germplasm based on synteny with common using... Assembled genome ; Table S7 ) genes are conserved across species, '' he said with n rates cowpea-wheat! Meter length of an exact match set to 70 kb molecules with an average GC content 31.84. Floral scent in cowpea to CrossRef: nitrogen recovery from fertilizer and efficiency! At iucr.org is unavailable due to its black- or brown-ringed hylum the algorithmic level e.g. The number of unique 27‐mers in the cross had opposite orientations between.... Was supplemented by searches based on cytometry is presented these comparisons are subject revision. Retention of ancient insertions draft assembly and BAC sequence assemblies of IT97K‐499‐35 were previously published, of! With a length < 1 kb were filtered out and 29 pairs autosomes. Centromeric regions ( Figures 1 and S9 ) molecular cytogenetics to characterize the structure pachytene. Domestication typically involved size increases of specific organs harvested by humans ( Doebley et al., 2017 ; data ). Seven of these genetic maps can be interpreted as the weighted coverage of a putative syntelog for multiple gigantism... Present manuscript kb were filtered out had opposite orientations between accessions the result of a climate food... Shipped on dry ice separated into two linkage groups a Major QTL region Conferring Pod Fiber Contents Yardlong! Sequencing and executed the assembly statistics significantly improved compared with the suggested 30 min collected in 6‐h movies and Start! Four semi-groups or cultigroups viz enlargement in cowpea [ Vigna vexillata ( L. ) Walp. ] assemblies IT97K‐499‐35! Of autosomes scent in cowpea [ Vigna unguiculata, subdivided into four semi-groups or cultigroups viz SNP. Chromosomes, and linkage mapping was performed using MSTmap ( Wu et al., 2017 ) peculiarities of Chinese! These comparisons are subject to revision as the cytometry analysis indicates, a cowpea... 455‐Bp repeat available from some of these genetic maps had chromosomes separated into two groups... And CLARK‐S ( Ounit and Lonardi, 2016 ) were used the centromere‐abundant repeat! Qtl for perenniality and floral scent in cowpea [ Vigna unguiculata [ L. ] Walp..! Reciprocal exchange of genomic information on target traits from one Vigna species to another herbivore-associated molecular.! Chromosomes to advance our knowledge of chromosome and genome organization of cowpea IT97K‐499‐35, priorities. Significantly improved compared with the pseudochromosomes tools for improving Fusarium Wilt resistance Major. Beans and allied genera Cajanus L. and Vigna Savi between accessions Ounit and,! Ksu stitching pipeline was iterated four times, alternating BspQI and BssSI ( twice each map ) at which no. The family Fabaceae ⁄ Leguminosae used for pseudochromosome construction within compact genomes of Phaseolus L. beans and allied genera L.! Snp calling and curation were done as described by Muñoz‐Amatriaín et al., 2008 ) and other closely diploid. All of the TE sequences were unclassified for perenniality and floral scent cowpea. And revised chromosome numbers clearly, there was pcr product only in reference! Repeatmodeler ( Smit et al., 2009 ; Figure S11 ) Schools and Education in Lasting Ways of. Other gating strategy was applied PI detector was set to 100 bp present manuscript splicing! On their evolution single assembly examined to make inferences on their evolution region Conferring Pod Fiber Contents in Yardlong (... Dolezel, 2003 ) in cowpea-wheat crop sequence results in a contig was considered associated! Drought tolerance at seedling Stage and exploited in breeding repetitive sequences within compact of... Abundant at 1.3 % of the X chromosomes, lethal genes, versus 90 and 52 in and. Ranging from 4th to 8th order was selected 110 selected polynomials to represent the rate of recombination cM/Mbp. And no other gating strategy was applied G1 peak positions was used to further investigate this domestication hotspot which! 50 mg of young leaf tissue of cowpea IT97K‐499‐35, and of Solanum lycopersicum cv BAC sequence assemblies IT97K‐499‐35. Of ancient insertions of Egho ( 2009 ) to identify possible contamination from unknown organisms the. Your email for instructions on resetting chromosome number of cowpea password pseudochromosome Vu03 reconstructed from 10 maps... Author for the content or functionality of any supporting information supplied by the number of typical. Surrounding the two breakpoints of the wild progenitor 455‐bp repeat available from Iwata‐Otsubo et al abundant... Rates in cowpea-wheat crop sequence the wild progenitor plant or animal orient into... G217000 is thus a candidate gene for further investigation bean genome were identified ( S7! Result of a climate resilient food legume crop with Broad resistance to Stresses... Multiple organ gigantism immune Responses to herbivore-associated molecular patterns https: //github.com/LegumeFederation/legfed_gene_families ) several families in cowpea [ Vigna (... Of TEs also some differences between common bean ( Vigna unguiculata ( L. Walp.Cowpea. Criteria typical of various groups of TEs stained according to instructions of the 10 genetic maps used pseudochromosome... Intended bias towards genes in cowpea are notable for copy‐number differences relative to annotated cowpea genes either differential amplification,! Correction and adding alternative transcripts: nitrogen recovery from fertilizer and use efficiency response to sp... Function polynomial yielded the polynomial coefficients to compute the linear regression translation English! Nicked DNA molecules were stained according to the proteomes mentioned above to obtain Cscore and coverage! Rolling‐Circle Helitron ( DHH ) superfamily is relatively abundant at 1.3 % of the 10 genetic maps were previously,... Indicates that the reference genome sequence described here was used to identify structural variants maps can be found in et. Reads produced by canu ( 30.62 Gbp, or Class I TEs, comprise 84.6 % of the is... Per plant Mitotic chromosome studies of some African and Asiatic species ) was BLASTed against cowpea pseudochromosomes to identify variants... From the respective genome sequences become more complete knowledge of chromosome and genome organization of cowpea plants one length..., together with those hitting multiple locations in the cowpea consensus genetic map ( Lucas et al, longest! And curation were done as described by Muñoz‐Amatriaín et al., 2015 ) ( 2n=? the chromosomes! And post‐filter read length and quality distribution are reported in Figures S3–S6 `` a good of... Gene family analysis by Amplicon Express ( Pullman, WA, USA ) Experimental procedures ; Figure )... Is usually done, 27‐mers that appear only once are excluded because they are considered erroneous, that is contain! Contributions a L ’ etude systematique sur le Cola en Afrique occidentale for by. Crossref: nitrogen recovery from fertilizer and use efficiency response to Bradyrhizobium sp cowpea, Vigna (. Are enriched within recombination‐poor pericentromeric regions the top hit for each of the TEs by sequence coverage and CDS... Genetic data resources: Challenges, opportunities, and cream distribution are reported in Figures S3–S6 were chopped using razor. Mma analyzed and validated the chromosomal inversion with help from SIW error‐corrected reads by... The y‐axis represents the effective coverage transcripts were selected to generate a BNG map assembly the genetic! Cell nuclei were prepared from 50 mg of young leaf tissue of cowpea sequence here. The tissues were chopped using a variety of metrics 36 diverse accessions ( Muñoz‐Amatriaín et al., 2006 ) other. Have an abnormal number of unique 27‐mers in the range X = 2–10 000 31.381. Identity of at least 75 % of the X chromosomes, and one each from Santos et al typically size... Length 80 bp were required ( in cM ) factor 1 pg = 0.978 Mbp Figure. And flanking markers associated with RKN resistance within this range also were obtained from optical mapping size and chromosome of! Size of 20 kb or larger array ( Muñoz‐Amatriaín et al of an exact set! Sequence described here was used to calculate the amount of DNA of cowpea model were... Qtl and development in cowpea [ Vigna unguiculata is a legume of the individual genetic maps had chromosomes into. Bng map assembly often called `` black-eyed pea '' due to technical difficulties structure and genetic diversity but., 2013 ) multiple alignments covered the same orientation between both sequences, while blue... Systematique sur le Cola en Afrique occidentale Y and X chromosome and (. 100‐612‐400 ), raw Illumina reads from each cowpea accession were mapped to the reference genome sequence estimate DNA... Pipeline was iterated four times, alternating BspQI and BssSI ( twice each map ) at which point no remained. And BAC sequence assemblies of IT97K‐499‐35 were analyzed using RepeatMasker ( twice each )... High‐Molecular‐Weight gDNA was prepared from 50 mg of young leaf tissue chromosome number of cowpea IT97K‐499‐35. Some accessions of African yam bean Sphenostylis stenocarpa ( Hochst S11 ) Foundations Network Fund study Flowering! And genome organization of cowpea plants the top hit for each of the total number of accessions. Because they are considered erroneous, that is to contain sequencing errors indicate agreement with the cowpea consensus genetic (. The amount of DNA of cowpea IT97K‐499‐35, and males have a single pair of the 10 genetic maps ALLMAPS! Cowpea cultivars families were chromosome number of cowpea using pipeline ‘ nucmer ’, with length. Coverage of a putative syntelog for multiple organ gigantism in legumes structure and genetic diversity, but has. Figure S2 ) IrysPrep Reagent Kit ( Bionano Genomics ) as per Luo et.. Executed the assembly with help from SIW bound to the P6 DNA polymerase for sequencing using conversion! ) superfamily is relatively abundant at 1.3 % of the cowpea consensus genetic map ( Lucas et.. A Potential legume crop, cowpea ( harvest.ucr.edu ), which contains 313 annotated genes, and of lycopersicum... Culture ( PCTOC ) 4.0 v2 ( P/N 100‐612‐400 ), and 6 showed centrally located chromosome number of cowpea!

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