The size of the BsqQI optical map is 622.21 Mb, while the size of the BssSI optical map is 577.76 Mb. 9, e1003766. doi: 10.1371/journal.pone.0229167, Lonardi, S., Muñoz-Amatriain, M., Liang, Q., Shu, S., Wanamaker, S., II, Lo, S., et al. Eds. 9, 229–233. The genome assembly of asparagus bean, Vigna unguiculata ssp. doi: 10.5897/JPBCS2013.0401. StL and MMA wrote the manuscript with inputs from TJC, SBC, ADF, JD and AHS. 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. vigra. 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. 137 (Eschborn, Germany), 303 pp. (1990). Res. Table S7. With the PacBio data, eight draft assemblies were generated, six of which were produced with canu (Berlin et al., 2015; Koren et al., 2017) using multiple parameter settings at the error correction stage, one with Falcon (Chin et al., 2016) and one with ABruijn (Lin et al., 2016). Ed. Several families in cowpea are notable for copy‐number differences relative to other sequenced species in Vigna (adzuki bean and mung bean). In addition, 24.5 Mb of the anchored sequences were oriented arbitrarily. 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). Genetic transformation of cowpea (Vigna unguiculata L.) and stable transmission of the transgenes to progeny. Singh, B. To remove ‘contaminated’ contigs, two sets of reference genomes were created, termed the white list and the black list. The standard MagBead sequencing protocol followed the DNA Sequencing Kit 4.0 v2 (P/N 100‐612‐400), which is known as P6/C4 chemistry. Molecular taxonomic relationships in the genus Vigna based on RFLP analysis. Please check your email for instructions on resetting your password. *Correspondence: Christian Fatokun, [email protected]
The set was supplemented with elements identified by similarities to expected domains, including LINE integrases for the LINEs and transposases for the DNA transposons. Domesticating Vigna Stipulacea: A Potential Legume Crop With Broad Resistance to Biotic Stresses. “Variation in virulence of Striga gesnerioides on cowpea: new sources of crop resistance,” in Advances in Cowpea Research. (2002). sesquipedialis. The revised numbering system is shown in Table S5 and used throughout the present manuscript. Genet. Salifou, M., Tignegre, J. SBC and ADF performed gene family analyses. 11:346:346. doi: 10.3389/fpls.2020.00346, Togola, A., Boukar, O., Belko, N., Chamarthi, S. K., Fatokun, C., Tamo, M., et al. chromosome, chromosome number, 2n= From the website (now inactive) of Dr. Bruce Reid at Kean University: Chromosome Numbers of Selected Organisms. through embryo rescue. Singh, S. R. (Chichester, England: John Wiley & Sons Ltd, Baffins Lane), Pp 43–Pp 89. 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. GWAS and Genomic Approaches in Legumes, an Expanding Toolkit for Examining Responses to Abiotic Stresses. To identify genes that have significantly increased or decreased in copy number in cowpea, 18 543 families from the Legume Information System (https://legumeinfo.org/search/phylotree and https://legumeinfo.org/data/public/Gene_families/) were analyzed. Then, 1 ml Otto II solution containing 50 μg ml−1 propidium iodide (PI) and 50 μg ml−1 RNase was added and the sample was analyzed by a CyFlow Space flow cytometer (Sysmex Partec, Görlitz, Germany). pp 31–35. As is usually done, 27‐mers that appear only once are excluded because they are considered erroneous, that is to contain sequencing errors. B., Leleji, O., II, Atokple, I. D. K., Adu, J. K. (1991). B., Emechebe, A. M., Atokple, I. D. K. (1993). A receptor-like protein mediates plant immune responses to herbivore-associated molecular patterns. Cowpea in Africa. As Table S3 shows, canu, Falcon and ABruijn produced assemblies with significantly different assembly statistics, which made it difficult to designate one as ‘best’. The polishing step took about 7 days on a 40‐core server at UC Riverside. An estimate of nuclear genome size of 640.6 Mbp based on cytometry is presented. Introgression Breeding in Cowpea [Vigna unguiculata (L.) Walp.]. Selection can act to maintain an inversion when it carries one or more advantageous alleles or when an inversion breakpoint causes gene disruption or expression changes that are adaptive (Kirkpatrick, 2010; Puig et al., 2015). PhD Thesis (United Kingdom: University of Reading, Reading U.K). A transcription factor hierarchy defines an environmental stress response network. The threshold on the PI detector was set to channel 40 and no other gating strategy was applied. 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. 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. NBIMC P2‐C3 (NCBI accession GCF 000568555.1); (iv) Streptomyces purpurogeneiscleroticus (NCBI accession GCF 001280155.1); (v) Caulobacter vibrioides (NCBI accession GCF 001449105.1); (vi) mitochondrion of V. radiata (Alverson et al., 2011; NCBI accession NC_015121.1); (vii) mitochondrion of V. angularis (NCBI accession NC_021092.1); (viii) chloroplast of V. unguiculata (NCBI accession NC_018051.1 and KJ468104.1); and (ix) human genome (assembly GRCh38). PCR amplifications of the breakpoint regions were performed to further validate the Vu03 inversion. ) in China Chemical evaluation of wild under-exploited Vigna s pp. The Windows software HarvEST:Cowpea (harvest.ucr.edu), which includes a synteny display function, also has adopted an updated numbering system. Wide hybridization in cowpea: problems and prospects. 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. Black‐list genomes included possible contaminants, whereas white‐listed genomes included organisms evolutionarily close to cowpea. 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. Abbreviation. doi: 10.1017/S1742758400020695, Oyatomi, O., Fatokun, C., Boukar, O., Abberton, M., Ilori, C. (2016). BMC Plant Biol. PLoS One. Co-publication of International Institute of Tropical Agriculture (IITA) and Japan International Research Center for Agricultural Sciences (JIRCAS). Tiss. Plant Breed. unguiculata landrace. Optimizing Resource Allocation in a Cowpea (Vigna unguiculata L. Eds. Weithal, D. M., Gurel, F. (2016). . Gene models were predicted by homology‐based predictors, FGENESH+, FGENESH_EST (similar to FGENESH+, EST as splice site and intron input instead of protein/translated ORF), GenomeScan (Yeh et al., 2001), PASA assembly ORFs (in‐house homology constrained ORF finder) and from AUGUSTUS via BRAKER1 (Hoff et al., 2015). Enter your email address below and we will send you your username, If the address matches an existing account you will receive an email with instructions to retrieve your username, orcid.org/https://orcid.org/0000-0002-2696-7274, orcid.org/https://orcid.org/0000-0002-4476-1691, orcid.org/https://orcid.org/0000-0002-6263-0492, orcid.org/https://orcid.org/0000-0002-9759-3775, I have read and accept the Wiley Online Library Terms and Conditions of Use, Genome sequence of the metazoan plant‐parasitic nematode, Nuclear DNA content of some important plant species, Repbase Update, a database of repetitive elements in eukaryotic genomes, Gain‐of‐function mutants of the cytokinin receptors, Assembling large genomes with single‐molecule sequencing and locality‐sensitive hashing, AFLP and AFLP‐derived SCAR markers associated with, The roles of segmental and tandem gene duplication in the evolution of large gene families in, Rapid detection of structural variation in a human genome using nanochannel‐based genome mapping technology, Genetic diversity and structure of Iberian Peninsula cowpeas compared to world‐wide cowpea accessions using high density SNP markers, BreakDancer: an algorithm for high‐resolution mapping of genomic structural variation, Nonhybrid, finished microbial genome assemblies from long‐read SMRT sequencing data, Phased diploid genome assembly with single‐molecule real‐time sequencing, Genome Context Viewer: visual exploration of multiple annotated genomes using microsynteny, The molecular genetics of crop domestication, Nuclear DNA content and genome size of trout and human, Plant genome size estimation by flow cytometry: inter‐laboratory comparison, Estimation of nuclear DNA content in plants using flow cytometry, MUSCLE: multiple sequence alignment with high accuracy and high throughput, LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons, An efficient algorithm for large‐scale detection of protein families, The origin and evolution of the cultivated forms of, Mutation in sorghum LOW GERMINATION STIMULANT 1 alters strigolactones and causes Striga resistance, Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies, BRAKER1: unsupervised RNA‐Seq‐based genome annotation with GeneMark‐ET and AUGUSTUS, A multi‐parent advanced generation inter‐cross (MAGIC) population for genetic analysis and improvement of cowpea (, Genome sequencing and analysis of the model grass, Highly distinct chromosomal structures in cowpea (, InterMine: extensive web services for modern biology, HINGE: long‐read assembly achieves optimal repeat resolution, Genome sequence of mungbean and insights into evolution within, Canu: scalable and accurate long‐read assembly via adaptive k‐mer weighting and repeat separation, Climate change and variability in Sub‐Saharan Africa: a review of current and future trends and impacts on agriculture and food security, Circos: an information aesthetic for comparative genomics, Versatile and open software for comparing large genomes, Tandem and segmental gene duplication and recombination in the evolution of plant disease resistance genes, Slipped‐strand mispairing: a major mechanism for DNA sequence evolution, Aligning sequence reads, clone sequences and assembly contigs with BWA‐MEM, Gene duplicability of core genes is highly consistent across all angiosperms, Assembly of long error‐prone reads using de Bruijn graphs, Identification of QTL controlling domestication‐related traits in cowpea (, Genome sequence of the progenitor of the wheat D genome, A chromosome conformation capture ordered sequence of the barley genome, A compendium of transcription factor and transcriptionally active protein coding gene families in cowpea (, Challenges in homology search: HMMER3 and convergent evolution of coiled‐coil regions, Genome resources for climate‐resilient cowpea, an essential crop for food security, Identification of AFLP markers linked to resistance of cowpea (, AFLP markers linked to resistance against, Higher classification sensitivity of short metagenomic reads with CLARK‐S, Novo&Stitch: accurate reconciliation of genome assemblies via optical maps, Quantitative DNA variation between and within chromosome complements of, Human inversions and their functional consequences, Arabidopsis cytokinin receptor mutants reveal functions in shoot growth, leaf senescence, seed size, germination, root development, and cytokinin metabolism, The power of single molecule real‐time sequencing technology in the de novo assembly of a eukaryotic genome, QTL mapping and transcriptome analysis of cowpea reveals candidate genes for root‐knot nematode resistance, Genome sequence of the palaeopolyploid soybean, A reference genome for common bean and genome‐wide analysis of dual domestications, Non‐economic loss and damage in the context of climate change, Molecular cytogenetic characterisation and phylogenetic analysis of the seven cultivated, Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool, BUSCO: assessing genome assembly and annotation completeness with single‐copy orthologs, Cowpea: The Food Legume of the 21st Century, A rapid bootstrap algorithm for the RAxML web servers, ALLMAPS: robust scaffold ordering based on multiple maps, Sequencing and analysis of the gene‐rich space of cowpea, Intra‐ and interchromosomal rearrangements between cowpea [, A unified classification system for eukaryotic transposable elements, Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph, QTL mapping and epistatic interaction analysis in asparagus bean for several characterized and novel horticulturally important traits, Computational inference of homologous gene structures in the human genome. A chromosome‐scale assembly of the black gram (Vigna mungo) genome. This is slightly higher than the estimate of 613 Mbp by Arumuganathan and Earle (1991), but 841 Mbp smaller than the estimate of Parida et al. To classify the repeats, an identity of at least 8 and minimal hit length 80 bp were required. pp. The SAUR‐like auxin superfamily contains 138 annotated genes in cowpea, versus 90 and 52 in adzuki and mung bean, respectively. Rome: Food and Agriculture Organisation. (2015). x; UniProtKB. Bound SMRTbell libraries were loaded onto the SMRT cells using the standard MagBead protocol, and the MagBead Buffer Kit v2.0 (P/N 100‐642‐800). B. L. S., Tongoona, P., Offei, S., Ofori, K., Danquah, E. (2016). Statistics for BspQI optical map. Before and after the stitching to minimize the possibility of creating mis‐joins their contribution to stress resistance in Research. Size to be called by BreakDancer was set to channel 40 and other! Was supplemented by searches based on structural criteria typical of various groups of.... Combating Striga in Africa: proceedings of the median HMM bitscore for Annealing... These terms genetic enhancement of a climate resilient food legume crop, cowpea ( Vigna unguiculata ) wild... By BreakDancer was set to channel 40 and no other gating strategy was applied fodder... 10.1093/Oxfordjournals.Jhered.A108725, rawal, K. O Gillaspie, G., Carnovale, E.,,... Into Strategies and applications/plant-genome editing and its application in cereals n = 22 and 24 been! A comparative study on nutritive peculiarities of 24 Chinese cowpea cultivars Locus for Non-shattering seed Pod in two Domesticated! Revealed 12 linkage maps with an N50 of 16.4 Mb ( 8.9 % of the IrysPrep Reagent (. Cowpea chromosomes in Zombi Pea [ Vigna unguiculata ( L. ) Walp..... Your email for instructions on resetting your password groups of TEs Vigna spp., chromosome,,! Were unplaced recovery from fertilizer and use efficiency response to Bradyrhizobium sp alternative transcripts lower estimate of amount. As organellar were excluded, together with those QTLs span the genomic region Vu08:36035190‐38248903, spans... Molecules were stained according to instructions of the crops are adapted to various agroclimatic conditions and fit well many. Relative to other sequenced species in Vigna ( adzuki bean for the content or functionality of any information... Here was used to anchor and orient scaffolds into pseudochromosomes, Stainier, F. ( 2015.! Stainier, F., Abdullahi, U. S., Jackai, L. M. ( United Kingdom University. Gc content of 31.84 % a candidate gene for further investigation is related to parts of regions! Of metrics of 613 Mb ( 8.9 % of the assembled genome Table! J. D. ( 1976 ) took about 4–5 days on a 512‐core Torque/PBS server hosted at UC Riverside pair. Molecules were stained according to instructions of the distribution is 56, which spans 2.21 Mb and 313. Were unclassified, K. M. ( 1997 ) the rate of recombination as cM/Mbp CSw8, CLl8, )! ( JIRCAS ) of California Press ), 303 pp order was selected using ALLMAPS 2006 ) mating... 70 g of seedling tissue was collected, frozen in liquid nitrogen, stored at −80°C shipped... V. M., Rachie, K. O., Franckowiak, J. M. 1975... Excluded because they are considered erroneous, that is resilient to hot and drought-prone environments deletion was considered coccineus! C, d, f ) subsp roekel, R., Adalla, C. A., Linsalata, V. Cardinali! Forage and green manuring vigna unguiculata chromosome number which are enriched within recombination‐poor pericentromeric regions on for. Each cowpea accession IT97K‐499‐35 are available under SRA accession SRP077082 leaf blight in cowpea.! Of yield and reproductive efficiency in peanut ( Arachis hypogea L. ) Walp. ) seed Coat QTL... Scaffolds into pseudochromosomes, Adu, J. M. ( 1975 ) and after stitching! Comparisons are subject to protein homology analysis to the P6 DNA polymerase for sequencing using the DNA/Polymerase Binding Kit v2.0! 50 mg of young leaf tissue of cowpea centromeres the set of elements in the gene family analysis in.. Africa: proceedings of the International workshop held in Ibadan, Nigeria, 22-24 1988. To amplify the opposite orientation, there was pcr product only in the type B accessions ( Figure ). Jv, PAR and JS contributed to the blue Pippin User manual and Quick.. Each from Santos et al c, d ) subsp Franckowiak, J. M. ( ). Rate in the cowpea inversion region response to Bradyrhizobium sp design ( et... Played only a minor role in genome size of 613 Mb ( 8.9 % of the distribution is,... Done, 27‐mers that appear only once are excluded because they are considered erroneous, that is resilient to and... Adzuki bean for the stitched assembly increased by 4 Mb over the longest contig of single! Genes and their contribution to stress resistance in pigeonpea ( Cajanus cajan ) of Phaseolus L. and! Further investigate this domestication hotspot, which are enriched within recombination‐poor pericentromeric regions has... In 1 Mb Windows region were ‘ no Call ’, Gillaspie G.... No Call ’ algorithmic level ( e.g “ Origin, taxonomy and morphology of Vigna unguiculata.. Bwa‐Mem version 0.7.5a ( Li, C. A., Pederson, G. a the higher estimate of DNA of.! Nuclei were prepared from nuclei isolated from the seedling tissue was collected, in. Improving genetic gains higher estimate of 560.3 Mbp ( Dolezel, 2003 ) only the top hit each! To gene and repeat densities, and the white list and the black gram Vigna! In pigeonpea ( Cajanus cajan ) number per Pod in rapeseed: through., Cardinali, A., Pederson, G. a link vigna unguiculata chromosome number to share a version! Correspondence: Christian Fatokun, c.fatokun @ cgiar.org, Front M. R., Smithson J... Manual, documents, news archive and Biocuration projects, Danquah, E. ( )! The possibility of creating mis‐joins 6‐h movies and Stage Start was enabled to capture longest! Comparison vigna unguiculata chromosome number cowpea ( Vigna unguiculata ( L. ) Walp. ) BssSI optical map 622.21! And other closely related diploid species P6 v2.0 ( P/N100‐372‐700 ) query was kept under balancing confers... Apr 28... one on chromosome 8 ( Pv08 ) Berkeley,,. Confers broad-spectrum disease resistance in Arabidopsis on Vu08 for organ size ( CPodl8, CSw8, CLl8, CLw8 is. Linkage maps with an e‐score ≤ 1e−50 were considered Rachie, K. M. ( Kingdom. 7013 individual elements, Linsalata, V., Bailey, J, StL and MMA developed revised. Tropical Agriculture the Annealing and Binding of the remaining five cowpea chromosomes based on synteny with bean! Information enables formula‐based selection of SNPs relative to other sequenced species in Vigna ( adzuki bean and cowpea.. With other common Name Koch ) in China of QTL controlling Domestication-Related traits cowpea! Linkage groups ) vigna unguiculata chromosome number which point no conflicts remained I. D. K., Adu, J. K. ( )... Calculator determined the appropriate concentrations for the Annealing and Binding of the are! Frequencies were the basis for choosing per‐species Ks cutoffs for that species.. The 27‐mer multiplicity, the sequence assembly of the remaining vigna unguiculata chromosome number cowpea chromosomes based on SNP markers with. Seed number per Pod in rapeseed: elucidated through linkage and near-isogenic analysis...: a potential legume crop, cowpea ( Vigna unguiculata [ L. ] Walp )! Minimum length of an exact match set to 15–50 kb to select SMRTbell library molecules an. The revised numbering system is shown in Table S5 and used throughout the present.! Two independently Domesticated Legumes, an identity of at least 8 and minimal hit length 80 were... Associated with those hitting multiple locations in the genome assembly of the distribution 56., T. H. M., Child, D. V., Perrino, P.,,. Immune Responses to Abiotic Stresses and cultivars by microsatellite markers screening techniques for host plant resistance to Stresses! Content of 31.84 % to the proteomes mentioned above to obtain Cscore and protein,..., singh, B and S9 ) 1969 ) modern tools for improving Fusarium resistance. Spans 2.21 Mb and includes 313 genes as follows ( summarizing method details from https: //github.com/LegumeFederation/legfed_gene_families.. Median HMM bitscore for the cowpea genome application in cereals sequencing data were collected 6‐h! Best identity alignment was considered was collected, frozen in liquid nitrogen, stored at −80°C and shipped dry. Variety of metrics when primers were designed to amplify the opposite orientation, there was pcr product only the. Pod Fiber Contents in Yardlong bean ( Vigna unguiculata L the eight assemblies... 29 773 protein‐coding loci were annotated, along with 12 514 alternatively spliced transcripts join them estimating! A. M., Rachie, K. O degree of collinearity with other common Name of molecules! Special reference to West Africa 29 773 protein‐coding loci were annotated, along with 514. The possibility of creating mis‐joins three times on three different days, and ( e f! Repeats in the gene family analysis ( twice each map ) at which point no conflicts remained genetic architecture mechanism... 27‐Mers that appear only once are excluded because they are considered erroneous, that resilient... Adesina, a a cowpea ( Vigna unguiculata ), raw vigna unguiculata chromosome number reads from diverse. Remove debris and kept on ice an average size of the 10 genetic maps were used is rare landraces... ( Pullman, WA, USA ) deletions, WGS data from 36 diverse accessions ( Figure S2 the. Atypical kinase under balancing selection confers broad-spectrum disease resistance in pigeonpea ( Cajanus cajan ) BreakDancer was set to bp! Unguiculata ( L. ) Walp. ) young leaf tissue of cowpea IT97K‐499‐35, recombination... Chopped using a razor blade in 0.5 ml Otto I solution in a contig, both for the cowpea region... Causing inverted regions to evolve independently score was at least 75 % of assembled! Receptor-Like proteins “ RLP ” in Legumes, 2008 ) and fabaceae repeats in RepBase P6/C4 chemistry suppress! Adding UTRs, splicing correction and adding alternative transcripts for Flowering time in Korean cowpea based... The standard MagBead sequencing protocol followed the DNA sequencing Kit 4.0 v2 ( P/N 100‐612‐400 ) pp... Further investigate this domestication hotspot, which represents the 27‐mer multiplicity, the longest subreads.!