Highly distinct chromosomal structures in cowpea (Vigna unguiculata), as revealed by molecular cytogenetic analysis

Iwata‐Otsubo, Aiko; Lin, Jer-Young; Gill, Navdeep; Jackson, Scott A.

doi:10.1007/s10577-015-9515-3

Cited by 30 publications

(35 citation statements)

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“…Hence, cowpea pseudochromosomes and all genetic maps were inverted for chromosomes Vu06, Vu10 and Vu11 to meet the convention of short arm on top and long arm on the bottom, corresponding to ascending cM values from the distal (telomeric) end of the short arm through the centromere and on to the distal end of the long arm. It is also of some interest that both Vu06 and Pv06 are acrocentric chromosomes, but although Pv09 is acrocentric the ratio of short to long arm in Vu09 (formerly cowpea linkage group 8) is 25.86–46.35 μm (Iwata‐Otsubo et al ., ). Clearly, there are many structural similarities but also some differences between common bean and cowpea chromosomes.…”

Section: Resultsmentioning

confidence: 97%

“…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 ., ). Regions containing this sequence span over 20.18 Mb (3.9% of the assembled genome; Table S7).…”

Section: Resultsmentioning

confidence: 97%

“…Landscape of the cowpea genome. (a) Cowpea chromosomes in Mb, with red lines representing centromeric regions based on a 455‐bp tandem repeat alignment (Iwata‐Otsubo et al ., ). (b) Recombination rate at each 1 Mb.…”

Section: Resultsmentioning

confidence: 97%

“…However, there was only one optimum solution to the chromosome numbering of cowpea, assigning Vu08 to previous cowpea linkage group/chromosome #5 and assigning Vu05 to previous linkage group/chromosome #1 (Table S5). In addition, comparisons between cowpea genetic maps and chromosomal maps developed by fluorescence in situ hybridization (FISH) using cowpea BACs as probes (Iwata‐Otsubo et al ., ) revealed that the prior orientations of three linkage groups (now referred to as Vu06, Vu10 and Vu11) were inverted relative to their actual chromosome orientation. Hence, cowpea pseudochromosomes and all genetic maps were inverted for chromosomes Vu06, Vu10 and Vu11 to meet the convention of short arm on top and long arm on the bottom, corresponding to ascending cM values from the distal (telomeric) end of the short arm through the centromere and on to the distal end of the long arm.…”

Section: Resultsmentioning

confidence: 99%

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The genome of cowpea (Vigna unguiculata [L.] Walp.)

et al. 2019

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SummaryCowpea (Vigna unguiculata [L.] Walp.) is a major crop for worldwide food and nutritional security, especially in sub‐Saharan Africa, that is resilient to hot and drought‐prone environments. 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. A total of 519 Mb is included in the assembled sequences. Nearly half of the assembled sequence is composed of repetitive elements, which are enriched within recombination‐poor pericentromeric regions. 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. 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. 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. The genome sequence facilitated the identification of a putative syntelog for multiple organ gigantism in legumes. A revised numbering system has been adopted for cowpea chromosomes based on synteny with common bean (Phaseolus vulgaris). An estimate of nuclear genome size of 640.6 Mbp based on cytometry is presented.

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Section: Resultsmentioning

confidence: 97%

Section: Resultsmentioning

confidence: 97%

Section: Resultsmentioning

confidence: 97%

Section: Resultsmentioning

confidence: 99%

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The genome of cowpea (Vigna unguiculata [L.] Walp.)

et al. 2019

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“…In Cowpea (Vigna unguiculata [L.] Walp), 11 distinct chromosomal structures were identified using chromosome-specific bacterial artificial chromosome clones for FISH, allowing for the analysis of heterochromatin distribution, centromere position, chromosome lengths, and positions of various rDNA regions (Iwata-Otsubo et al, 2016). In Brachypodium distachyon root-tip cells, chromosomal aberrations were analyzed using multicolor FISH during chemical mutageninduced micronuclei formation.…”

Section: Advancement Of Cytogenetic Techniquesmentioning

confidence: 99%

Dynamic Changes in Plant Nuclear Organization in Response to Environmental and Developmental Signals

et al. 2017

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ORCID ID: 0000-0002-4141-5400 (I.M.).In both plants and animals, the nucleus acts as an organizing center for the changes that occur during an organism's life cycle, whether as part of a developmental program or in response to environmental factors. Here, we cover recent research that explores roles of the nucleus other than gene expression in light response, fertilization, plant-pathogen interactions, bacterial symbiotic events, and hormone signaling. New strides have been made in understanding subnuclear organization, how nuclear organization responds to different environments and developmental stages, and how the cytoplasm-nucleoplasm connections are made that allow these responses. We further highlight new tools that have been developed to study dynamic changes in nuclear organization.The nucleus is compartmentalized by a double membrane called the nuclear envelope (NE), which consists of the outer nuclear membrane (ONM), the inner nuclear membrane (INM), and the embedded nuclear pore complexes (NPCs). The NPC is the primary pathway of macromolecular transport between the nucleus and the cytoplasm and is conserved throughout eukaryotes. The ONM and INM are populated by a variety of membrane-associated proteins, and in particular the inner membrane hosts a specific subset of proteins (Starr and Fridolfsson, 2010;Meier et al., 2017). In addition to functioning in nuclear morphology, chromatin attachment, and likely signal transduction, plant NE-associated proteins are involved in nuclear positioning and movement within the larger cellular context (Griffis et al., 2014). While plant nuclear ultrastructure reveals an inner nuclear membrane-associated meshwork similar to the animal lamina, plant genomes do not encode obvious lamin homologs. Instead, plant-specific long coiled-coil proteins with structural similarity to animal lamins might contribute to this meshwork. Plants also lack centrosomes, and the NE plays a role as the microtubuleorganizing center at the onset of mitosis. NE proteins functioning as calcium channels are involved in perinuclear calcium oscillations, which are an important step in the establishment of plant-symbiont interactions (recently reviewed in Meier et al., 2017).While the nuclear periphery is emerging as an essential organizing platform for the nucleus, intranuclear functional and structural organization might also originate from independent self-assembly processes, with the most conspicuous manifestation of these processes revealed as the nucleolus. New methods are now robustly adapted for plants to reveal greater details of functional nuclear and nucleolar organization. Due to the increasing realization that spatial organization is a crucial part of biological function at the subcellular level, many of these aspects have been recently reviewed

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A view of the pan‐genome of domesticated Cowpea (Vigna unguiculata [L.] Walp.)

et al. 2023

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Cowpea, Vigna unguiculata L. Walp., is a diploid warm-season legume of critical importance as both food and fodder in sub-Saharan Africa. This species is also grown in Northern Africa, Europe, Latin America, North America, and East to Southeast Asia. To capture the genomic diversity of domesticates of this important legume, de novo genome assemblies were produced for representatives of six subpopulations of cultivated cowpea identified previously from genotyping of several hundred diverse accessions. In the most complete assembly (IT97K-499-35), 26,026 core and 4963 noncore genes were identified, with 35,436 pan genes when considering all seven accessions. GO terms associated with response to stress and defense response were

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Highly distinct chromosomal structures in cowpea (Vigna unguiculata), as revealed by molecular cytogenetic analysis

Cited by 30 publications

References 83 publications

The genome of cowpea (Vigna unguiculata [L.] Walp.)

The genome of cowpea (Vigna unguiculata [L.] Walp.)

Dynamic Changes in Plant Nuclear Organization in Response to Environmental and Developmental Signals

A view of the pan‐genome of domesticated Cowpea (Vigna unguiculata [L.] Walp.)

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