Dataset Information

Isolation and identification of EST-SSR markers in Ixonanthes chinensis (Ixonanthaceae).

ABSTRACT: Premise:Ixonanthes (Ixonanthaceae) consists of between three and 19 species, among which I. chinensis and I. khasiana are considered vulnerable. Here, 58 microsatellite markers were developed for further conservation of these two Ixonanthes species. Methods and Results:RNA transcripts of I. chinensis were sequenced and assembled into 19,545 unigenes, and 994 simple sequence repeat (SSR) loci were identified from 920 contigs. Based on these, 106 primer pairs were designed, 58 were successfully amplified, and 12 demonstrated polymorphism among five populations. The number of alleles per locus varied from three to 10, and the levels of observed and expected heterozygosity ranged from 0.000 to 1.000 and 0.000 to 0.844, respectively. Further assessment of the transferability of the 58 amplifiable primers reported 30 being successfully cross-amplified in I. icosandra and three in Erythroxylum sinense. Conclusions:These novel SSR markers will be useful for future genetic conservation studies on these Ixonanthes species.

SUBMITTER: Guo W

PROVIDER: S-EPMC6526656 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

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Isolation and identification of EST-SSR markers in <i>Ixonanthes chinensis</i> (Ixonanthaceae).

Guo Wei W Fan Qiang Q Wang Jinjiang J Meng Kaikai K Chen Sufang S Zhu Liping L Liao Wenbo W

Applications in plant sciences 20190510 5

<h4>Premise</h4><i>Ixonanthes</i> (Ixonanthaceae) consists of between three and 19 species, among which <i>I. chinensis</i> and <i>I. khasiana</i> are considered vulnerable. Here, 58 microsatellite markers were developed for further conservation of these two <i>Ixonanthes</i> species.<h4>Methods and results</h4>RNA transcripts of <i>I. chinensis</i> were sequenced and assembled into 19,545 unigenes, and 994 simple sequence repeat (SSR) loci were identified from 920 contigs. Based on these, 106 p ...[more]

PMID: 31139512

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Project description:Mung bean (Vigna radiate (L.) Wilczek) is an important traditional food legume crop, with high economic and nutritional value. It is widely grown in China and other Asian countries. Despite its importance, genomic information is currently unavailable for this crop plant species or some of its close relatives in the Vigna genus. In this study, more than 103 million high quality cDNA sequence reads were obtained from mung bean using Illumina paired-end sequencing technology. The processed reads were assembled into 48,693 unigenes with an average length of 874 bp. Of these unigenes, 25,820 (53.0%) and 23,235 (47.7%) showed significant similarity to proteins in the NCBI non-redundant protein and nucleotide sequence databases, respectively. Furthermore, 19,242 (39.5%) could be classified into gene ontology categories, 18,316 (37.6%) into Swiss-Prot categories and 10,918 (22.4%) into KOG database categories (E-value < 1.0E-5). A total of 6,585 (8.3%) were mapped onto 244 pathways using the Kyoto Encyclopedia of Genes and Genome (KEGG) pathway database. Among the unigenes, 10,053 sequences contained a unique simple sequence repeat (SSR), and 2,303 sequences contained more than one SSR together in the same expressed sequence tag (EST). A total of 13,134 EST-SSRs were identified as potential molecular markers, with mono-nucleotide A/T repeats being the most abundant motif class and G/C repeats being rare. In this SSR analysis, we found five main repeat motifs: AG/CT (30.8%), GAA/TTC (12.6%), AAAT/ATTT (6.8%), AAAAT/ATTTT (6.2%) and AAAAAT/ATTTTT (1.9%). A total of 200 SSR loci were randomly selected for validation by PCR amplification as EST-SSR markers. Of these, 66 marker primer pairs produced reproducible amplicons that were polymorphic among 31 mung bean accessions selected from diverse geographical locations. The large number of SSR-containing sequences found in this study will be valuable for the construction of a high-resolution genetic linkage maps, association or comparative mapping and genetic analyses of various Vigna species.

Dataset Information

Isolation and identification of EST-SSR markers in Ixonanthes chinensis (Ixonanthaceae).

Publications

Isolation and identification of EST-SSR markers in <i>Ixonanthes chinensis</i> (Ixonanthaceae).

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