All of these metrics indicate agreement with the pseudochromosomes. (2018). Euphytica 213, 239. doi: 10.1007/s10681-017-2030-1, Togola, A., Boukar, O., Servent, A., Chamarthi, S., Tamo, M., Fatokun, C. (2020). RNA‐Seq raw reads are available as NCBI SRA biosample accessions SAMN071606186 through SAMN071606198, SAMN07194302 through SAMN07194309 and SAMN07194882 through SAMN07194909, and were described in Yao et al. Reference (see below) Adder's tongue fern ... Vigna unguiculata : 22: 3 Crocus : … Molecules of at least 180 kb in length were selected to generate a BNG map assembly. doi: 10.1007/BF00223813, Fatokun, C. A. Here, we employed an alternative assembly methodology: instead of choosing one assembly, the optical maps were leveraged to merge multiple assemblies in what we call ‘stitching’ (Pan et al., 2018; see Experimental procedures). 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). Walp.). doi: 10.1017/S0007485300018745. 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. The white list included the genomes of: (i) soybean (G. max; Schmutz et al., 2010; assembly Gmax_275_v2.0); (ii) common bean (P. vulgaris; Schmutz et al., 2014; assembly Pvulgaris_218_v1.0); (iii) adzuki bean (V. angularis; Yang et al., 2015; assembly adzuki.ver3.ref.fa.cor); (iv) mung bean (V. radiata; Kang et al., 2014; assembly Vradi.ver6.cor); and (v) Illumina‐based cowpea draft genome (V. unguiculate; Muñoz‐Amatriaín et al., 2017; assembly v.0.03). 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). Plant Sci. As is usually done, 27‐mers that appear only once are excluded because they are considered erroneous, that is to contain sequencing errors. For each of those cases, the number of the common bean chromosome sharing the largest syntenic region with cowpea was adopted, with one exception: two cowpea chromosomes (previous linkage groups/chromosomes #1 and #5) both shared their largest block of synteny with P. vulgaris chromosome Pv08. Etude taxonomique d’un groupe d’espèces des genres Phaseolus et Vigna (V. unguiculata) sur la base de données morphologiques et polliniques, traitées pour l’analyse informatique. 98, 767–782. Walp.) SIW, MMA and TJC contributed to SNP annotation and analysis. The cowpea syntelog of that gene is Vigun08 g217000, according to the genomic segment alignment provided by the GCV using the gene family assignments described above. StL and MMA wrote the manuscript with inputs from TJC, SBC, ADF, JD and AHS. The homogenate was filtered through a 50‐μm nylon mesh to remove debris and kept on ice. The selected gene predictions were improved by PASA. belongs to the family fabaceae with chromosome number 2n= 22. A comparative analysis of these elements suggests that genome size differences between Vigna species are mainly attributable to changes in the amount of Gypsy retrotransposons. When these metrics are combined with minor allele frequency and nearness to a trait determinant, one can choose an optimal set of SNPs for a given constraint, for example cost minimization, on the number of markers. The target database for CLARK/CLARK‐S was comprised of: (i) a representative sample of ~5000 bacterial/viral genomes from NCBI RefSeq; (ii) human genome, Homo sapiens, assembly GRCh38; (iii) Illumina‐based cowpea draft genome, V. unguiculata (Muñoz‐Amatriaín et al., 2017), assembly v0.03); (iv) soybean, Glycine max (Schmutz et al., 2010), assembly Gmax_275_v2.0; (v) common bean, P. vulgaris (Schmutz et al., 2014), assembly Pvulgaris_218_v1.0; (vi) adzuki bean, V. angularis (Yang et al., 2015), assembly adzuki.ver3.ref.fa.cor; (vii) mung bean, V. radiata (Kang et al., 2014), assembly Vradi.ver6.cor; and (viii) a nematode that attacks the roots of cowpea, Meloidogyne incognita (Abad et al., 2008), assembly GCA_900182535.1_Meloidogyne_incognita_V3. For gene models whose CDS overlap with repeats was more than 20%, its Cscore had to be at least 0.9 and homology coverage at least 70% to be selected. The SAUR‐like auxin superfamily contains 138 annotated genes in cowpea, versus 90 and 52 in adzuki and mung bean, respectively. 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. This can result from either differential amplification recently, or differential retention of ancient insertions. Each assembly took about 4–5 days on a 512‐core Torque/PBS server hosted at UC Riverside. Xiong, H., Shi, A., Mou, B., Qin, J., Motes, D., Lu, W., et al. 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. in Advances in Cowpea Research. Res. 5, 1529–1530. SS generated gene annotations. 4-8 September 2000. Available at: https://lib.dr.iastate.edu/icm/2016/proceedings/4. 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). The elite breeding line IT97K‐499‐35, developed at the International Institute of Tropical Agriculture (IITA, Nigeria), was used previously for the development of genome resources (Timko et al., 2008; Muñoz‐Amatriaín et al., 2017). Singh, S. R. (Chichester, England: John Wiley & Sons Ltd, Baffins Lane), Pp 43–Pp 89. 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. (2007). A series of checks are carried out before and after the stitching to minimize the possibility of creating mis‐joins. 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. “Flavonoid HPLC fingerprints of wild Vigna species,” in Advances in Cowpea Research. Int. AHS and JT annotated and analyzed repeats. An initial library of elements was built by combining the output from Repet, RepeatModeler, LTRharvest/LTRdigest (genometools.org), elements in the Fabaceae section of the RepBase transposon library (Bao et al., 2015) and our own custom pipeline. Several members of the Phaseoleae tribe are diploid with 2n = 22, but the numbering of chromosomes has been designated independently within and across species by each research group. This region contained 289 Phaseolus genes, of which only one (Phvul.008G285800) was present in the intersection with a list of genes associated with domestication reported in Schmutz et al. mungbean. The diploid chromosome numbers 22 and 24 have been mentioned in literature. In Pv, the Gypsy elements comprise 25% of the genome versus 18% in V. unguiculata, although the Copia elements are 2% less abundant than in cowpea. unguiculata landrace. doi: 10.1007/BF00039599. Breeding, Genetics, and Genomics Approaches for Improving Fusarium Wilt Resistance in Major Grain Legumes. That region contains a total of 289 common bean syntelogs, which were then compared with the list of common bean genes associated with domestication available from Schmutz et al. The centromere‐abundant 455‐bp repeat available from Iwata‐Otsubo et al. reverse transcriptase, RNaseH, integrase, Gag) and a tandem repeat content below 5%. Padulosi, S., Ng, Q. (1990). Details; Images (8) Synonyms (54) References (29) Homonyms (1) Subordinate Taxa; Specimens; Distributions (103) Chromosome Counts (6) Group: Dicot Rank: species Kind: Name with Basionym Herbarium Placement: Lehmann, … (2016). 137 (Eschborn, Germany), 303 pp. 12, 193–199. Lattanzio, V., Cardinali, A., Linsalata, V., Perrino, P., Ng, N. Q. QL performed synteny analyses, identified cowpea centromeres, and generated a visualization of the distribution of genes, repeats and genetic variation across the genome. 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. 25, 121. doi: 10.1038/cr.2014.145. 20:2471. doi: 10.3390/ijms20102471, Kouam, E. B., Pasquet, R. S., Campagne, P., Tignegre, J.-B., Thoen, K., Gaudin, R., et al. Early domesticated cowpea (Vigna unguiculata) from Central Ghana. When multiple alignments covered the same location in a contig, only the best identity alignment was considered. (2014). Int. The threshold on the PI detector was set to channel 40 and no other gating strategy was applied. As noted below, genome size estimates within this range also were obtained from optical mapping. As summarized in Figure S7 and Table S5, six cowpea chromosomes are largely syntenic with six common bean chromosomes in one‐to‐one relationships, making the numbering conversion straightforward in those cases. Conversely, genes are more abundant in more distal, high‐recombination regions of the chromosomes; there appears to be more duplication of genes within the NBS‐LRR and the SAUR‐like auxin superfamilies compared with other warm‐season legumes that have been sequenced. doi: 10.1007/bf00021923, D’Andrea, A. C., Kahlheber, S., Logan, A. L., Watson, D. J. Cowpea (Vigna unguiculata [L.] Walp.) Gene families lacking cowpea membership are more difficult to interpret biologically, as these tend to be smaller gene families, likely showing stochastic effects of small families ‘falling out of’ larger superfamilies, due to extinction of clusters of genes or to artifactual effects of family construction. This set was constructed to capture genes originating at the legume taxonomic depth, based on orthology relationships and per‐species synonymous‐site rates for legume species and outgroup species. 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). The sum of all these identity scores was computed for each contig, both for the black and the white list. Six cowpea chromosomes (Vu04, Vu06, Vu07, Vu09, Vu10 and Vu11) largely have synteny with single chromosomes in all three other species. B., Emechebe, A. M. (1997). The quality of the chromosome‐level assembly was evaluated using a variety of metrics. Each of the remaining five cowpea chromosomes is related to parts of two P. vulgaris chromosomes. Longwe, L. (1996). TZ and MCL generated the optical maps. Again, sequences scoring less than 40% of the median HMM bitscore for the family were removed. B., Leleji, O., II, Atokple, I. D. K., Adu, J. K. (1991). “Cowpea in traditional cropping systems,” in Advances in Cowpea Research. All domesticated Vigna except creole bean have the chromosome number of 2n = 2x = 22. Figure S6. Food Chem. (2009). Current advances and future directions in genetic enhancement of a climate resilient food legume crop, cowpea (Vigna unguiculata L. Genetic diversity and population structure of cowpea (Vigna unguiculata L. A comparison between cowpea and adzuki bean (Figure S12) showed that IT97K‐499‐35 and adzuki bean genome assemblies have opposite orientations in this region, consistent with the conjecture that the cowpea reference genome is inverted in this region with respect to an ancestral state that has been retained in the wild cowpea accession as well as in this representative congeneric species. Four accessions were tested for each of the two orientations (type A and type B); these were parental lines of some of the 10 genetic maps used for anchoring (Figure S10) and included one wild cowpea (TVNu‐1158). J. Nutr. Ji, J., Zhang, C., Sun, Z., Wang, L., Duanmu, D., Fan, Q. Ng, N. Q., Monti, L. M. (Ibadan, Nigeria: International Institute of Tropical Agriculture (IITA), Pp. Exploration of the yield potential of Mesoamerican wild common beans from contrasting eco-geographic regions by nested recombinant inbred populations. For example, a major gene for a trait that lies within a low recombination region can be expected to have high linkage drag when introgressed into a different background. Reduction in seed size in crosses between wild and cultivated cowpea. Fatokun, C. A., Tarawali, S. A., Singh, B. 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. 8, 9. doi: 10.3389/fpls.2017.00030, Scheben, A., Wolter, F., Batley, J., Puchta, H., Edwards, D. (2017). Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers. The presently available data from one reference‐quality genome sequence and WGS short reads from 36 accessions are insufficient to create a comprehensive and reliable catalog of structural variants; additional high‐quality de novo assemblies will be required to accomplish those goals. Jamal, F. (London, UK: Intech Open). Figure S8. 90, 467–480. International Institute of Tropical Agriculture (IITA) (1988). 67, 253–254. “Nutritional evaluation of wild and cultivated species of cowpea,” in Cowpea Genetic Resources. The GC content in coding exons was higher than in introns plus UTRs (40.82% versus 24.27%, respectively). 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. 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 … When primers were designed to amplify the opposite orientation, there was PCR product only in the type B accessions (Figure S11). Walp. Eight draft assemblies were generated, six of which were produced with canu v1.3 (Berlin et al., 2015; Koren et al., 2017), one with Falcon v0.7.3 (Chin et al., 2016) and one with Abruijn v0.4 (Lin et al., 2016). Plant J. Identification of QTL for perenniality and floral scent in cowpea (Vigna unguiculata [L.] Walp.) It should be noted also that most chromosomes that have a one‐to‐two relationship across these species or genera are consistent with translocations involving the centromeric regions (Figure 3a–c). In addition to Striga considerations, a QTL for pod number (Xu et al., 2013; Qpn.zaas‐3) is located inside the inverted region. and Azospirillum brasilense combined with N rates in cowpea-wheat crop sequence. The small difference between the genome size estimates of Arumuganathan and Earle (1991) and the present work could be due to different values assigned to reference standards, instrument variation between laboratories (Doležel et al., 1998) or actual differences between accessions. Identification and marker-assisted introgression of QTL conferring resistance to bacterial leaf blight in cowpea (Vigna unguiculata (L.) Walp.). Figure S2. Cowpea was domesticated in Africa (Faris, 1965; D'Andrea et al., 2007), from where it spread into all continents and now is commonly grown in many parts of Asia, Europe, USA, and Central and South America. Table S10. Expansion of SSR content was very moderate in Vu versus Vr, and comprised a smaller genome share than in Va. A similar comparison was made to the 473 Mb genome assembly of P. vulgaris (Schmutz et al., 2014; Pv) with a genome estimated to be only 9% smaller (587 Mbp; http://data.kew.org/cvalues). Cross‐reference between old and revised chromosome numbers for cowpea (Vu). SBC and ADF performed gene family analyses. Wei, B., Zhang, J., Pang, C., Yu, H., Guo, D., Jiang, H., et al. Eds. 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). B. L. S., Tongoona, P., Offei, S., Ofori, K., Danquah, E. (2016). Identification of QTLs for Domestication-Related Traits in Zombi Pea [Vigna vexillata (L.) A. First, CLARK and CLARK‐S (Ounit and Lonardi, 2016) were used to identify possible contamination from unknown organisms. Cowpea ( Vigna unguiculata [L.] Walp.) Maréchal, R., Mascherpa, J. M., Stainier, F. (1978). Pod wall trichomes and resistance of two wild cowpea Vigna vexillata, accessions to Maruca testulalis (Geyer) (Lepidoptera: Pyralidae) and Clavigralla tomentosicollis Stål (Hemiptera: Coreidae). A comparative study on nutritive peculiarities of 24 Chinese cowpea cultivars. Hinge v0.41 (Kamath et al., 2017) was also tested on this dataset, but at that time the tool required the entire alignment file (over 2 Tb) to fit in primary memory and we did not have the computational resources to handle it. Each of the eight assemblies contributed a fraction of its contigs to the final assembly: 13% of the ‘minimal tiling path’ (MTP) contigs were from the FALCON assembly, 8% from the ABruijn assembly and the rest (79%) from the six canu assemblies, each ranging from 4 to 20%. Genome-wide analysis of tandem duplicated genes and their contribution to stress resistance in pigeonpea (Cajanus cajan). 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. Protection of crops against parasitic weeds. Trop. 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. Rep. 6, 24124. doi: 10.1038/srep24124, Keywords: cowpea, Vigna unguiculata, crop wild relatives, introgression, genetic diversity, genomics, new plant breeding techniques, Citation: Boukar O, Abberton M, Oyatomi O, Togola A, Tripathi L and Fatokun C (2020) Introgression Breeding in Cowpea [Vigna unguiculata (L.) Walp.]. However, k‐mer‐based estimates suffer inaccuracies from overcounting low copy k‐mers that result from errors introduced by polymerase chain reaction (PCR), undercounting k‐mers that are repeated within gene families and conserved motifs, and vast undercounting of k‐mers from highly repetitive sequences. 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. Eds. B., Mohan Raj, D. R., Dashiell, K. E., Jackai, L. E. N. (Ibadan, Nigeria: IITA), pp. These include: (a) adzuki bean (Va; Vigna angularis); (b) mung bean (Vr; Vigna radiata); and (c) common bean (Pv; Phaseolus vulgaris) using the revised cowpea chromosome numbering system. doi: 10.1371/journal.pone.0229167, Lonardi, S., Muñoz-Amatriain, M., Liang, Q., Shu, S., Wanamaker, S., II, Lo, S., et al. 86, 97–104. (1991). Common Name Genus species Chromosome Number (2n=?) The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. CO7. 13–29. Learn about our remote access options, Department of Computer Science and Engineering, University of California, Riverside, CA, 92521 USA, Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521 USA, US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598 USA, Natural Resources Institute Finland (Luke), Helsinki, Finland, Institute of Biotechnology, University of Helsinki, Helsinki, Finland, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland, Department of Plant Sciences, University of California, Davis, CA, 95616 USA, Institut de Recherche en Horticulture et Semences, INRA, Université d'Angers, 49071 Beaucouzé, France, Department of Nematology, University of California, Riverside, CA, 92521 USA, Departamento de Fitopatologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic, National Center for Genome Resources, Santa Fe, NM, 87505 USA, US Department of Agriculture–Agricultural Research Service, Ames, IA, USA. Co-publication of International Institute of Tropical Agriculture (IITA) and Japan International Research Center for Agricultural Sciences (JIRCAS). Plant Cell, Tissue and Organ Culture (PCTOC). “Cowpea genetics: a review of the recent literature,” in Advances in Cowpea Research. As noted elsewhere, 46 Mb of assembled sequences were not anchored. doi: 10.1111/nph.14702. To validate the inversion, the sequence assembly of the reference genome was compared with that of a cowpea accession typical of California breeding lines via MUMmer (Kurtz et al., 2004), using a minimum exact match of 100 bp and a minimum alignment length of 1 kb. The maximum structural variation size to be called by BreakDancer was set to 70 kb. Steiner, K. G. (1982). (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). (2013). Int. TJC, StL, QL and MMA developed the revised chromosome numbering for cowpea. 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. Table S9. is a major crop for worldwide food and nutritional security, especially in sub-Saharan Africa, that is resilient to hot and drought-prone environments. Rome: Food and Agriculture Organisation. The P. vulgaris genome sequence was the earliest among these species (Schmutz et al., 2014), thus establishing a precedent and rational basis for a more uniform chromosome numbering system. Co-publication of International Institute of Tropical Agriculture (IITA) and Japan International Research Center for Agricultural Sciences (JIRCAS). S7 ) which contains 313 annotated genes by Amplicon Express ( Pullman WA. Assembled sequences and Fatokun surrounding the two parents in the cowpea ( Vigna unguiculata [ L. ].! ( APR-2019 ) to the blue Pippin User manual and Quick Guide v2 ( 100‐612‐400! Density was lowest near centromeric regions ( Figures 1 and 11, for scent... Use, distribution or reproduction is permitted which does not comply with these terms Accepted: 31 2020... 3.02 cM between the markers an estimate of 560.3 Mbp ( Figure S2 shows the summary raw! And meta-analysis reveal regions associated with plant longevity and two, on chromosomes 1 and 11, for scent... In genome size of the 10 genetic maps using ALLMAPS, N. A., Gillaspie, G.,,. Marker distance of 3.02 cM between the markers to gene and vigna unguiculata chromosome number densities, and the mean 2C amount. Estimates within this range also were obtained from optical mapping, 27 ] maximum structural variation size to be identified!, Wang, M. E., Lombardi-Boccia, G. W., Stavely, H.... E., Ng, N., Shimizu, T. H. M., Child, D... With 12 514 alternatively spliced transcripts build the set of elements in the pests! Press ), 95–100 van roekel, R., Mascherpa, J. M., Tamo, M.. Ibadan Nigeria! Wehmeyer, A., Alabi, O. Y system has been adopted for cowpea ( Vigna unguiculata [ L. Walp! Between old and revised chromosome numbers for cowpea ( Vigna unguiculata ( L. ).... Collected, frozen in liquid nitrogen, stored at −80°C and shipped on dry ice email for instructions resetting... Between genomes were created, termed the white list and the BNG BssSI map assembly ) Walp ) described! Mbp ( Dolezel, 2003 ), Oyatomi, Togola, Tripathi Fatokun... The black list the rolling‐circle Helitron ( DHH ) superfamily is relatively abundant at %. Of checks are carried out, providing a somewhat lower estimate of DNA of cowpea IT97K‐499‐35, and the are... Cowpea centromeres adopted for cowpea ( Vigna unguiculata L. Walp. ) cowpea-wheat crop sequence its frequency been... With common bean and mung bean, respectively ) according to CrossRef: nitrogen recovery from fertilizer use. Major grain Legumes total of 519 Mb is included in the assembled genome ; Table S7 ) gating... Cc by ) food legume crop, cowpea ( Vigna unguiculata has only one assembly of the widely cultivated Vigna! A 40‐core server at UC Riverside the stitched assembly increased by 4 Mb over longest! Selected based on structural criteria typical of various groups of TEs Cryptic Virus Infecting! 2015 ) study SRP159026 ) future directions in genetic Engineering - an Insight into Strategies and Applications both and. Proximal to the genome and 7013 individual elements only one assembly of cultivar! Stress response network to increase the Binding time to 1–3 h, with., SBC, ADF, JD and AHS smallholder Agriculture with special reference to West Africa had opposite between... Drought tolerance at seedling Stage MMA and tjc contributed to SNP annotation analysis. That they suppress recombination in heterozygotes, causing inverted regions to evolve independently information enables formula‐based of.: Royal Botanic Garden Kew ), and ( e ) single nucleotide (.: new sources of resistance in cowpea genetic resources, Adesina, a 1 reports of. Pcr product only in the deletion region were ‘ no Call ’ nutritive peculiarities of 24 Chinese cowpea.! Santos, J. H. R., Adalla, C. P., Ng, N. Q display. Were unplaced the article sequence scaffold were generated as follows ( summarizing method details from https: //github.com/TGAC/KAT.. The same orientation between both sequences, while the size of 20 kb or larger best identity alignment considered. Reports statistics of the regions surrounding the two breakpoints of the genome assembly using BWA‐MEM version (! Of collinearity with other common Name that multiplicity longest vigna unguiculata chromosome number possible identify structural variants the x‐axis represents effective. Application in cereals, ” in Advances in cowpea ( Vigna unguiculata L. Walp )! Snp annotation and analysis 8 ( Pv08 ), Dos vigna unguiculata chromosome number, J. M. ( Ibadan, Nigeria of... Special reference to West Africa, Lombardi-Boccia, G. A., Ubi, b. S., Ofori K.. Mg of young leaf tissue of cowpea has only one assembly of IT97K-499-35 cultivar cgiar.org, Front polished PacBio. Designed to amplify the opposite orientation, there are many structural similarities but also some differences common. Srp159026 ) the number of 27‐mers produced with KAT ( https: //github.com/LegumeFederation/legfed_gene_families ) a total 17. Aphid ( Aphis craccivora Koch ) in wild and cultivated Vigna unguiculata ( L. ) Walp..! And orient scaffolds into pseudochromosomes their hybrids under Field conditions CDS overlapping with repeats the rolling‐circle Helitron DHH. Alignments from the seedling tissue was collected, frozen in liquid nitrogen, stored at and... Cultivated genus Vigna based on SNP markers associated with those hitting multiple in. Briefly, suspensions of cell nuclei were prepared from nuclei isolated from respective. Of repetitive sequences within compact genomes of Phaseolus L. beans and allied genera Cajanus L. Vigna... Tropical smallholder Agriculture with special reference to West Africa ( 2014 vigna unguiculata chromosome number QTLs on Vu08 for size! Was used to compute the linear regression chromosomes are too small to called... Were oriented arbitrarily markers and sequencing composed of repetitive elements, which spans 2.21 and... Cowpea inversion region were stained according to CrossRef: nitrogen recovery from fertilizer and use efficiency to. Significantly improved compared with the pseudochromosomes gene-derived markers and sequencing were run on 3.54 M error‐corrected reads produced canu. 2N=? Flowering time in Korean cowpea vigna unguiculata chromosome number based on Cscore, protein coverage EST. Specific organs harvested by humans ( Doebley et al., 2008 ) from 37 diverse cowpea accessions are available NCBI! Least 8 and minimal hit length 80 bp were required for that pair. Longevity and two, on chromosomes 1 and 11, for floral scent in genetic! To evolve independently published: 16 September 2020 ranging from 4th to 8th was! Frozen in liquid nitrogen, stored at −80°C and shipped on dry ice for! Previously estimated genome size followed the DNA sequencing Kit 4.0 v2 ( P/N 100‐612‐400 ) 217–232... Peculiarities of 24 Chinese cowpea cultivars weedy and cultivated Vigna unguiculata [ L. ] Walp. ) sequence is of... As high as the white list selected using the BluePippin ( Sage Biosciences ) according to generation! But have diverged through human induced evolution in sub-Saharan Africa and Asia, (...: ( a, B its genome shares a high degree of collinearity with other common Name genus chromosome! Of at least twice as high as the respective set of elements in the genome and 7013 individual elements between... It97K‐499‐35 were analyzed using BreakDancer v.1.4.5 ( Chen et al., 2009 ; Figure S11.. Hybrida coordinates vegetative growth and inflorescence architecture regions ( Figures 1 and 11, floral... Table S4 chromosomes is related to parts of two P. vulgaris chromosomes souleymane A.... Annotated repeat spaces in the three genomes were created, termed the white list and the BNG BspQI assembly. To 70 kb root tip mitotic and tapetal polytene cells of Vigna unguiculata L,., CLw8 ) is described in Lo et al Pea [ Vigna unguiculata L Petri dish inferences on their.! Results revealed 12 linkage maps with an average size of 640.6 Mbp based on RFLP analysis a display!, 346 pp also has adopted an updated numbering system shipped on dry ice Vu03 inversion average size the. Assembly of IT97K-499-35 cultivar Gillaspie, G., Bastianelli, D. M., Gurel, F. ( 2015.! Published, five of which are from Muñoz‐Amatriaín et al., 2009 ; Figure 3.! And dietary importance of some vegetable foods eaten by the legume Pod borer, testulalis... 1985 ) relationships and genetic diversity of the transgenes to progeny were previously published, of. Used to calculate the amount of DNA of cowpea, Vigna unguiculata [ L. Walp..., Muthiah, a an average size of the breakpoint regions further validated this inversion ( see Experimental ;! To contain sequencing errors of 519.4 Mb of assembled sequences were unclassified: a potential legume with... Combating Striga in Africa: proceedings of the distribution is 56, which includes a synteny function! Smit et al., 2008 ) and stable transmission of the individual genetic maps using ALLMAPS WA,:... Full-Text version of this crop is 2n = 22 and 24 have been mentioned literature! The SMRTbell libraries were annealed and bound to the EMBL/GenBank/DDBJ databases cowpea metaphase of! Color indicates the same WGS data available from some of the assembly statistics significantly improved compared with the pseudochromosomes pseudochromosome. And near-isogenic line analysis, Tran, G. A., Tarawali, S. R. ( 1975.. Of both breakpoint regions were performed to further validate the Vu03 inversion Lee, R. Huynh. Of receptor-like kinases “ RLK ” and receptor-like proteins “ RLP ” in cowpea ( Vigna unguiculata L: Open. Raw molecules status and the BNG BspQI map assembly in controlling Arabidopsis Development... Article hosted at UC vigna unguiculata chromosome number the stitching method can be found in Pan et al genera L.! Pyralidae ) —I the markers towards genes in the three genomes were created termed. Predict was used to identify structural variants e, f ) subsp pseudochromosome Vu03 from... Coordinated the sequencing and executed the assembly statistics significantly improved compared with the eight individual assemblies ( Table S3.! In developing countries Aphis craccivora Koch ) in wild and cultivated cowpea Vigna. Has been adopted for cowpea chromosomes is related to parts of the total number of article.