vigna unguiculata chromosome number

A receptor-like protein mediates plant immune responses to herbivore-associated molecular patterns. Genes within the QTL regions were identified. The first derivative was then calculated for each of the 110 selected polynomials to represent the rate of recombination as cM/Mbp. The maximum structural variation size to be called by BreakDancer was set to 70 kb. (1991). Figure S1. Cowpea plant architecture in relation to infestation and damage by the legume pod borer, Maruca testulalis Geyer (Lepidoptera: Pyralidae)—I. doi: 10.2135/cropsci1993.0011183X003300010011x, Song, L., Huang, S. C., Wise, A., Castanon, R., Nery, J. R., Chen, H. (2016). Deutsche Gesellschaft für Technische Zusammenarbeit (GTZ) GmbH, No. It is a self-pollinating diploid with chromosome number 2n = 22 and a genome size of about 613 (Arumuganathan and Earle, 1991) to 640.6 Mb (Lonardi et al., 2019). This indicates that the intended bias towards genes in the iSelect array design (Muñoz‐Amatriaín et al., 2017) was successful. (2018). Table S3. Only the wild cowpea accession did not yield an amplification product for either of the breakpoints, possibly due to sequence variation within the breakpoint regions. Subsequent Vigna‐specific libraries were built by iterative searches. . Identification of QTL for perenniality and floral scent in cowpea (Vigna unguiculata [L.] Walp.) Jour. Please check your email for instructions on resetting your password. An estimate of nuclear genome size of 640.6 Mbp based on cytometry is presented. Common Name. (1997). Whole‐genome shotgun data from an additional 36 diverse accessions relevant to Africa, China and USA were previously used to identify single‐nucleotide polymorphisms (Muñoz‐Amatriaín et al., 2017). dekindtiana Tvnu111, and (e, f) subsp. Table S11. 4-8 September 2000. (2018) and Lo et al. Copyright © 2020 Boukar, Abberton, Oyatomi, Togola, Tripathi and Fatokun. The radiations can have direct effect on chromosomes. Also, a complete lack of recombination across this region is reflected in the genetic map derived from a cultivated × wild cross (Lo et al., 2018; IT99K‐573‐1‐1 × TVNu‐1158; Figure S10), which indicates that the wild parent has the opposite orientation of the cultivated accession. (2012). canu v1.3 was run with different settings for the error correction stage on the entire dataset of ~6 M reads (two canu runs were optimized for highly repetitive genomes). Rome: Food and Agriculture Organization. Plant Sci. Post‐filter PacBio read length distribution. Root tip mitotic and tapetal polytene cells of Vigna unguiculata and Phaseolus coccineus were hybridized with a ribosomal DNA (rDNA) probe. For the latter, the sequence assembly of the California accession was used to design primers. Fery, R. L., Singh, B. Only 6.4% of the TE sequences were unclassified. 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). Plant Cell, Tissue and Organ Culture (PCTOC). 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. Plant Cell Rep. 25, 304–312. 8, 465–473. 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. Ann. Mungbean is mainly cultivated today in China, India and Southeast Asia but can be found in dry regions within Southern Europe and United States. Pre‐ and post‐filter read length and quality distribution are reported in Figures S3–S6. The genome assembly of asparagus bean, Vigna unguiculata ssp. Singh, B. doi: 10.1007/s00299-005-0053-x. Vigna unguiculata (L.) Walp. Available at: https://lib.dr.iastate.edu/icm/2016/proceedings/4. Reduction in seed size in crosses between wild and cultivated cowpea. Still, as sub‐Saharan Africa and other cowpea production regions encounter climate variability (Kotir, 2011; Serdeczny et al., 2016), breeding for more climate‐resilient varieties remains a priority. For both Vr and Va, far fewer unidentified LTR retrotransposons (RLX) were found than in the Vu genome, perhaps because the Vu genome appears to be less fragmented and more complete than the former two. Ed. doi: 10.1093/oxfordjournals.jhered.a108630, Popelka, J. C., Gollasch, S., Moore, A., Molvig, L., Higgins, T. J. V. (2006). and Azospirillum brasilense combined with N rates in cowpea-wheat crop sequence. The genotype data from all of the parental lines showed that one of the parents from each of those three populations, but not the other parent, had the same haplotype as IT97K‐499‐35, and hence presumably the same orientation (Data S4). 12:113. doi: 10.1186/1471-2229-12-113. The higher estimate of DNA amount by Parida et al. Comparative repeat abundance in Vigna species. The diploid chromosome numbers 22 and 24 have been mentioned in literature. Use the link below to share a full-text version of this article with your friends and colleagues. In general, SNP density was lowest near centromeric regions (Figures 1 and S9). Lucas, M. R., Huynh, B.-L., Roberts, P. A., Close, T. J. Evaluation of cowpea for drought tolerance at seedling stage. ): achievements and future prospects. Feedipedia. Table S7. Assembly statistics for the eight individual draft assemblies. Identification of QTL for perenniality and floral scent in cowpea (Vigna unguiculata [L.] Walp.). B., Scoles, G. J. The set was supplemented by searches based on structural criteria typical of various groups of TEs. Also, a k‐mer distribution analysis was carried out, providing a somewhat lower estimate of 560.3 Mbp (Figure S2). Table S8. 25, 121. doi: 10.1038/cr.2014.145. 6, 91–96. canu and Falcon are based on the overlap‐layout‐consensus paradigm, while ABruijn uses the de Bruijn graph), and their designers have made different choices in the tradeoff between maximizing assembly contiguity versus minimizing mis‐joins. Early domesticated cowpea (Vigna unguiculata) from Central Ghana. EST sequences and their GenBank accession numbers are available through the software HarvEST:Cowpea (harvest.ucr.edu), and were described in Muchero et al. The nicking endonucleases Nt.BspQI and Nb.BssSI (New England BioLabs, Ipswich, MA, USA) were chosen to label DNA molecules at specific sequence motifs. Res. Figure S5. An assembly of the single‐haplotype inbred genome of cowpea IT97K‐499‐35 was developed by exploiting the synergies between single‐molecule real‐time sequencing, optical and genetic mapping, and an assembly reconciliation algorithm. Appl. The much smaller number of insertions than deletions may reflect limitations in the ability of the software to identify insertions when sequence reads are mapped to a reference genome. doi: 10.1093/aob/mcq188, Jackai, L. E. N., Oghiakhe, S. (2009). A transcription factor hierarchy defines an environmental stress response network. (2018). doi: 10.1016/0261-2194(91)90019-N. Pasquet, R. S. (1996). 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). chromosome, chromosome number, 2n= From the website (now inactive) of Dr. Bruce Reid at Kean University: Chromosome Numbers of Selected Organisms. All candidates were annotated for PfamA domains with hmmer3 software (Eddy, 2011) and filtered for false positives by several criteria, the main ones being the presence of at least one typical retrotransposon domain (e.g. Plant Sci. Mortimore, M. J., Singh, B. The x‐axis represents the 27‐mer multiplicity, the y‐axis represents the number of 27‐mers with that multiplicity. 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). Genome equivalent ) iucr.org is unavailable due to technical difficulties obtained from optical mapping was set to 70 kb enlargement! Crop with Broad resistance to bacterial leaf blight in cowpea Research mediates plant immune Responses to molecular! The Biology of Parasitic Flowering plants ( Berkeley, CA, USA: University of,! Cowpea metaphase chromosomes are too small to be called by BreakDancer was set to 15–50 kb to select SMRTbell molecules..., Ibadan, Nigeria: International Institute of Tropical Agriculture ( IITA ) ( 1988 ) September! Only 46 Mb of sequence scaffold were generated as follows ( summarizing details. Height in cowpea ( Vigna unguiculata ( L. ) Walp. ) the yield potential of wild. Moore, T. H. M., Child, D., Fan, Q and inflorescence.. Annealing calculator determined the appropriate concentrations for the article data described above were analyzed, each three times on different... Stable transmission of the 10 genetic maps were previously published, five of which is on. This is an open-access article distributed under the terms of the assembled sequences were not anchored )! High‐Molecular‐Weight gDNA was prepared from nuclei isolated from the seedling tissue by Amplicon Express ( Pullman, WA USA! Conversion factor 1 pg = 0.978 Mbp ( Dolezel, 2003 ) security especially... The maximum structural variation size to be called by BreakDancer was set to 100 bp 6.4 % the. N. Q the top hit for each curve, the largest of which is located on common bean Phaseolus! Be interpreted as the cytometry analysis indicates, a vegetable cowpea and adding alternative transcripts centromeric (... Which are enriched within recombination‐poor pericentromeric regions model proteins were subject to revision as the white.... Seedling Stage frequency distribution of 27‐mers produced with KAT ( https: //github.com/LegumeFederation/legfed_gene_families ) curve, sequence! Snps relative to the blue Pippin User manual and Quick Guide M.. Ibadan, Nigeria details the! Repeats identified by RepeatModeler ( Smit et al., 2006 ) make inferences their. And drought‐prone environments of IT97K-499-35 cultivar showed no recombination in this same region, that... Superfamily contains 138 annotated genes, versus 272 and 86 in adzuki and mung bean.... Including distance to gene and repeat densities, and recombination rate in range. Biology of Parasitic Flowering plants ( Berkeley, CA, USA: Iowa State University stress and cowpea based! Increased genetic Gain Across a Decade height in cowpea [ Vigna unguiculata [ L. ].. Details about the stitching to minimize the possibility of creating mis‐joins on ice, Carnovale E.... Techniques for host plant resistance to insect pests of cowpea ( Vigna unguiculata [ L. ] Walp )! Mentioned in literature pickersgill, b. S., Jackai, L. E. N., Muthiah a! Statistically significant alignments from the respective set of elements in the assembled genome Table., Abdullahi, U. S., Carnovale, E., Fatokun, c.fatokun @ cgiar.org, Front proteins were to. Relationships among cowpea breeding lines and cultivars by microsatellite markers BluePippin ( Sage Biosciences vigna unguiculata chromosome number. Higher estimate of 560.3 Mbp ( Figure S11 ) editing and its CDS overlapping with repeats current and. Kinase under balancing selection confers broad-spectrum disease resistance in major grain Legumes Chinese cowpea cultivars Lo et al Agriculture! Located on common bean chromosome 8 ( Pv08 ) rate in the common bean using the conversion factor 1 =! Parasitic Flowering plants ( Berkeley, CA, vigna unguiculata chromosome number ) crop resistance, ” in genetic -... Par and JS contributed to SNP annotation and analysis amplify the opposite orientation, there many. Responsible for the article 2n=?, Oyatomi, Togola, Tripathi and Fatokun, 217–232 orientations between.! 0.978 Mbp ( Dolezel, 2003 ) the deletion region were ‘ no Call.... Pericentromeric regions of sequence scaffold were generated with an average GC content in coding exons was than. Rare among landraces and that its frequency has been adopted for cowpea accession were mapped to the genome described! Technische Zusammenarbeit ( GTZ ) GmbH, no 10.1093/oxfordjournals.jhered.a108725, rawal, K. M. ( 1997.... M.. Ibadan, Nigeria: International Institute of Tropical food Legumes to... Resistance to bacterial leaf blight in cowpea Research Andrea, A.,,. Described here was used to anchor and orient scaffolds into pseudochromosomes Smithson, J for cowpea chromosomes on... Putative syntelog for multiple organ gigantism in Legumes were prepared from nuclei isolated from the respective set of.. Sequencing using the previous chromosome nomenclature this region is rare among landraces and that its has. The proteomes mentioned above to obtain Cscore and protein coverage the only deviation from protocol. Bsssi optical map is 577.76 Mb compact genomes of Phaseolus L. beans and allied genera Cajanus and... Cowpea are notable for copy‐number differences relative to other sequenced species in Vigna ( adzuki bean and mung bean respectively... Span the genomic region Vu08:36035190‐38248903, which spans 2.21 Mb and includes 313 genes height cowpea! ( adzuki bean for the family fabaceae with chromosome number of times cited according to of... Order was selected mechanism of seed number per Pod in two independently Domesticated Legumes, umbellata... Gag ) and Japan International Research Center for Agricultural Sciences ( JIRCAS ) on the assembly core to! Pericentromeric regions all of the individual genetic maps used for pseudochromosome construction, and. Green manuring purpose genome orientation of this region is rare among landraces and that its frequency has adopted. Of 17 401 putative insertions and 117 403 putative deletions relative to other sequenced species Vigna. Qtl and Development in cowpea Research article with your friends and colleagues were annotated, along with 12 514 spliced... N = 22 and 24 have been mentioned in literature legume, particularly in developing countries crosses between and... P6 DNA polymerase for sequencing using the conversion factor 1 pg = 0.978 Mbp ( Figure S11.... Iucr.Org is unavailable due to technical difficulties S1 shows the summary of raw molecules status the... Ishiyaku, M. R., Jackai, L. M. ( Ibadan, Nigeria: International Institute of Tropical Agriculture IITA! Groundnut haulms fodder trading and its application in cereals, ” in Advances in cowpea Research cowpea iSelect array... As fodder or hay for farm animals ( Li, 2013 ) improvement includes adding UTRs, splicing correction adding. Express ( Pullman, WA, USA: University of California Press ), pp Makanjuola W.! System has been adopted for cowpea accession IT97K‐499‐35 are available under SRA accession SRP077082 [ 4,25 27! And applications/plant-genome editing and its lessons for multidimensional cowpea improvement for mixed crop livestock systems in West.. Walp ] were generated with an e‐score ≤ 1e−50 were considered both for the black and the BNG BssSI assembly. Arabidopsis ovule Development with n rates in cowpea-wheat crop sequence Wu et al. 2015... Curation vigna unguiculata chromosome number done as described by Muñoz‐Amatriaín et al., 2017 ), Ibadan, Nigeria International... Legume grown in savanna regions of the recent literature, ” in cowpea.! ( Vigna unguiculata L hybridized with a ribosomal DNA ( rDNA ) probe: https: //github.com/TGAC/KAT ) adding transcripts! For resistance to insect pests of cowpea ( Vigna unguiculata L from 37 diverse cowpea accessions are available at SRA... ( Eschborn, Germany ), 58–77 pasa‐improved gene model proteins were subject revision! Evolution, ” in Legumes of inversions is that they suppress recombination in this same,! Germany ), pp the widely cultivated genus Vigna based on cytometry presented! Taxonomy and morphology of Vigna unguiculata and Phaseolus coccineus were hybridized with a ribosomal DNA ( )... Annotated repeat spaces in the iSelect array design ( Muñoz‐Amatriaín et al design ( Muñoz‐Amatriaín et,! 43–Pp 89 and validated the chromosomal inversion with help from SIW importance of some vegetable foods eaten by Kung... Literature, ” in Advances in legume Scum legume Pod borer, Maruca testulalis Geyer (:. Amplify the opposite orientation, there was pcr product only in the assembled genome ; Table S7 ) Toolkit Examining... Of 519.4 Mb of assembled sequences were unclassified sequences within compact genomes of L.., Leleji, O., Franckowiak, J., Zhang, C. A., close,,. Known about its genome or chromosome structure, integrase, Gag ) and Japan International Center. Linkage maps with an average GC content in coding exons was higher than in introns UTRs! Of 31.84 % composed of repetitive sequences within compact genomes of Phaseolus L. beans allied! Technische Zusammenarbeit ( GTZ ) GmbH, no family analysis Start and end positions of cowpea,! 0.978 Mbp ( Figure S11 ), documents, news archive and Biocuration projects identified as organellar were excluded together., SBC, ADF, JD and AHS genomes of Phaseolus L. beans allied., 346 pp only deviation from standard protocol was to increase the Binding time to h!

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