Mining and analysis of simple sequence repeats in the chloroplast genomes of genus Vigna

Shukla, Nidhi; Kuntal, Himani; Shanker, Asheesh; Sharma, Satyendra Nath

doi:10.1016/j.biori.2018.08.001

Cited by 15 publications

(12 citation statements)

References 51 publications

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“…Pod length (cm) of primers of cpSSRs allowed to verify a low level of polymorphism within the cultivated cowpeas, which is in agreement with previous studies reported for cowpea (Pan et al, 2014;Shukla et al, 2018) and other crops such as the common bean (Phaseolus vulgaris) (Desiderio et al, 2013).…”

Section: Accession Number Asupporting

confidence: 88%

Iberian Peninsula cowpea diversity: chloroplast, microsatellite and morpho-agronomic variability

Monteiro

Castro

Carvalho

et al. 2020

Systematics and Biodiversity

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Cowpea (Vigna unguiculata (L.) Walp.) is an important legume crop in Southern Europe and a valuable source of proteins, minerals, and vitamins. Moreover, cowpea has additional interest stemming from drought tolerance and high biological nitrogen fixation. In this research, the genetic diversity of cowpea landraces from Southern European countries was evaluated using molecular and morpho-agronomical approaches, with the objective of enhancing legumes diversity grown through sustainable cropping. A set of 10 chloroplast microsatellite primer pairs (cpSSRs) was used to evaluate genetic diversity and phylogenetic relationships among 113 Vigna accessions including Vigna unguiculata subsp. unguiculata, subsp. alba, subsp. pubescens, subsp. tenuis and var. spontanea and accessions from other Vigna species, as V. mungo, V. radiata and V. racemosa. This set of primers successfully established ten haplotypes, with the most frequent being shared by the V. unguiculata subsp. unguiculata cultigroups unguiculata and sesquipedalis and var. spontanea. Eight loci were polymorphic; nevertheless, a low level of polymorphism was verified within the cultivated cowpeas. Additionally, 10 agronomic traits were evaluated on cowpea landraces of the cultigroup unguiculata, mainly from Portugal. PCA clustered the landraces into three main groups, each one containing Portuguese landraces. Total seed weight per plant revealed the highest coefficient of variation, and 100 seed weight the highest heritability. The performed study shows the wide agro-morphological diversity still existing in cowpea in Iberian Peninsula and other Southern European countries, despite the low polymorphism detected in its chloroplast genome. The high variability detected in the collection of cowpea analysed and the sharing of haplotypes by cultivated and wild material is of great importance for breeding programs of this species.

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Section: Accession Number Asupporting

confidence: 88%

Iberian Peninsula cowpea diversity: chloroplast, microsatellite and morpho-agronomic variability

Monteiro

Castro

Carvalho

et al. 2020

Systematics and Biodiversity

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“…Microsatellites are small repeating units (1–6 nucleotide) within a genome nucleotide sequence ( Shukla et al, 2018 ). They exhibit polymorphism and are usually dominantly expressed at the species level hence used as DNA markers for the population and evolutionary studies ( Vendramin et al, 1999 ; Deguilloux et al, 2004 ; Piya et al, 2014 ; Redwan et al, 2015 ; Gao et al, 2018 ).…”

Section: Resultsmentioning

confidence: 99%

Complete Chloroplast Genomes of Acanthochlamys bracteata (China) and Xerophyta (Africa) (Velloziaceae): Comparative Genomics and Phylogenomic Placement

et al. 2021

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Acanthochlamys P.C. Kao is a Chinese endemic monotypic genus, whereas XerophytaJuss. is a genus endemic to Africa mainland, Arabian Peninsula and Madagascar with ca.70 species. In this recent study, the complete chloroplast genome of Acanthochlamys bracteata was sequenced and its genome structure compared with two African Xerophyta species (Xerophyta spekei and Xerophyta viscosa) present in the NCBI database. The genomes showed a quadripartite structure with their sizes ranging from 153,843 bp to 155,498 bp, having large single-copy (LSC) and small single-copy (SSC) regions divided by a pair of inverted repeats (IR regions). The total number of genes found in A. bracteata, X. spekei and X. viscosa cp genomes are 129, 130, and 132, respectively. About 50, 29, 28 palindromic, forward and reverse repeats and 90, 59, 53 simple sequence repeats (SSRs) were found in the A. bracteata, X. spekei, and X. viscosa cp genome, respectively. Nucleotide diversity analysis in all species was 0.03501, Ka/Ks ratio average score was calculated to be 0.26, and intergeneric K2P value within the Order Pandanales was averaged to be 0.0831. Genomic characterization was undertaken by comparing the genomes of the three species of Velloziaceae and it revealed that the coding regions were more conserved than the non-coding regions. However, key variations were noted mostly at the junctions of IRs/SSC regions. Phylogenetic analysis suggests that A. bracteata species has a closer genetic relationship to the genus Xerophyta. The present study reveals the complete chloroplast genome of A. bracteata and gives a genomic comparative analysis with the African species of Xerophyta. Thus, can be useful in developing DNA markers for use in the study of genetic variabilities and evolutionary studies in Velloziaceae.

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“…Considering the coverage of the SSRs and extendedSSRs on Korean isolate of the A. thaliana chloroplast genome (in total, 1,825 bp out of 154,464 bp; 1.18%), the expected number of sequence variations of the SSR and extendedSSR regions is 0.75; however, the number of common SSRs or extendedSSRs is 117 (81.82%), indicating that the numbers of sequence variations located in SSR or extendedSSR regions are lower than expected number (107.25 sequence variations for SSR or extendedSSR regions). These variations can be used to develop molecular markers [ 41 ].…”

Section: Resultsmentioning

confidence: 99%

The Complete Chloroplast Genome of Arabidopsis thaliana Isolated in Korea (Brassicaceae): An Investigation of Intraspecific Variations of the Chloroplast Genome of Korean A. thaliana

Park¹,

Xi²,

Kim³

2020

International Journal of Genomics

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Arabidopsis thaliana (L.) Heynh. is a model organism of plant molecular biology. More than 1,700 whole genome sequences have been sequenced, but no Korean isolate genomes have been sequenced thus far despite the fact that many A. thaliana isolated in Japan and China have been sequenced. To understand the genetic background of Korean natural A. thaliana (named as 180404IB4), we presented its complete chloroplast genome, which is 154,464 bp long and has four subregions: 85,164 bp of large single copy (LSC) and 17,781 bp of small single copy (SSC) regions are separated by 26,257 bp of inverted repeat (IRs) regions including 130 genes (85 protein-coding genes, eight rRNAs, and 37 tRNAs). Fifty single nucleotide polymorphisms (SNPs) and 14 insertion and deletions (INDELs) are identified between 180404IB4 and Col0. In addition, 101 SSRs and 42 extendedSSRs were identified on the Korean A. thaliana chloroplast genome, indicating a similar number of SSRs on the rest five chloroplast genomes with a preference of sequence variations toward the SSR region. A nucleotide diversity analysis revealed two highly variable regions on A. thaliana chloroplast genomes. Phylogenetic trees with three more chloroplast genomes of East Asian natural isolates show that Korean and Chinese natural isolates are clustered together, whereas two Japanese isolates are not clustered, suggesting the need for additional investigations of the chloroplast genomes of East Asian isolates.

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Mining and analysis of simple sequence repeats in the chloroplast genomes of genus Vigna

Cited by 15 publications

References 51 publications

Iberian Peninsula cowpea diversity: chloroplast, microsatellite and morpho-agronomic variability

Iberian Peninsula cowpea diversity: chloroplast, microsatellite and morpho-agronomic variability

Complete Chloroplast Genomes of Acanthochlamys bracteata (China) and Xerophyta (Africa) (Velloziaceae): Comparative Genomics and Phylogenomic Placement

The Complete Chloroplast Genome of Arabidopsis thaliana Isolated in Korea (Brassicaceae): An Investigation of Intraspecific Variations of the Chloroplast Genome of Korean A. thaliana

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