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Data set for transcriptome analysis of Apocynum venetum L.

ABSTRACT: In this paper, we present the transcriptome profiles of the A. venetum L. by RNA-Seq approach. A total of 6.57?Gb raw data were obtained, and 52,983 unigenes with an average length of 1009?bp and N50 of 1632?bp were annotated with the 7 databases. The unigenes annotated to KEGG database were divided into 21 categories from 6 main groups. Among these, 4952 (22.21%) unigenes were clustered to "Global and overview maps", and 1834 (8.23%) unigenes were clustered to "Carbohydrate metabolism". In addition, 6340 unigenes containing 7579 SSRs were identified and the mononucleotide, dinucleotide, trinucleotide motifs were the most common motif type (95.59%), accounting for 39.62%, 36.02%, and 19.95%, respectively.

SUBMITTER: Chen P

PROVIDER: S-EPMC6160392 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

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Data set for transcriptome analysis of <i>Apocynum venetum</i> L.

Chen Ping P Gao Gang G Yu Chunming C Chen Jikang J Chen Kunmei K Zhu Aiguo A

Data in brief 20180905

In this paper, we present the transcriptome profiles of the <i>A. venetum</i> L. by RNA-Seq approach. A total of 6.57 Gb raw data were obtained, and 52,983 unigenes with an average length of 1009 bp and N50 of 1632 bp were annotated with the 7 databases. The unigenes annotated to KEGG database were divided into 21 categories from 6 main groups. Among these, 4952 (22.21%) unigenes were clustered to "Global and overview maps", and 1834 (8.23%) unigenes were clustered to "Carbohydrate metabolism". ...[more]

PMID: 30271870

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Project description:BACKGROUND:Apocynum venetum L. is an important medicinal plant that is mainly distributed in the coastal areas and northwest of China. In addition to its high medical and economic value, its adaptation to saline-alkali and coastal saline lands makes A. venetum an ideal candidate for use in vegetation restoration. To date, the study of A. venetum has been limited in the northwest region of China, little attention has been paid to the genetic diversity and population structure of A. venetum populations in the coastal region. Here, we performed transcriptome sequencing of total RNA from A. venetum leaves and developed efficient expressed sequence tag-simple sequence repeat (EST-SSR) markers for analyzing the genetic diversity and population structure of A. venetum in the coastal region. RESULTS:A total of 86,890 unigenes were generated after de novo assembly, and 68,751 of which were successfully annotated by searching against seven protein databases. Furthermore, 14,072 EST-SSR loci were detected and 10,243 primer pairs were successfully designed from these loci. One hundred primer pairs were randomly selected and synthesized, twelve primer pairs were identified as highly polymorphic and further used for population genetic analysis. Population genetic analyses showed that A. venetum exhibited low level of genetic diversity (mean alleles per locus, NA?=?3.3; mean expected heterozygosity, HE?=?0.342) and moderate level of genetic differentiation among the populations (genetic differentiation index, FST?=?0.032-0.220) in the coastal region. Although the contemporary (mean mc?=?0.056) and historical (mean mh?=?0.106) migration rates among the six A. venetum populations were moderate, a decreasing trend over the last few generations was detected. Bayesian structure analysis clustered six populations into two major groups, and genetic bottlenecks were found to have occurred in two populations (QG, BH). CONCLUSIONS:Using novel EST-SSR markers, we evaluated the genetic variation of A. venetum in the coastal region and determined conservation priorities based on these findings. The large dataset of unigenes and SSRs identified in our study, combining samples from a broader range, will support further research on the conservation and evolution of this important coastal plant and its related species.

Dataset Information

Data set for transcriptome analysis of Apocynum venetum L.

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Data set for transcriptome analysis of <i>Apocynum venetum</i> L.

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