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Dataset of full-length transcriptome assembly and annotation of apocynum venetum using pacbio sequel II.

ABSTRACT: Apocynum venetum, which belongs to Apocynaceae, is widely distributed throughout salt-barren zones, desert steppes, and alluvial flats of the Mediterranean area and Northwestern China. Apocynum venetum has long been used in traditional Chinese medicine because of its anti-inflammation, anti-oxidative, anti-hypertensive, anti-cancer, and bactericidal effects. However, the absence of genetic information on Apocynum venetum is an obstacle to understanding its stress resistance or medicinal function. This work was aimed at generating a full-length transcriptome of Apocynum venetum using Pacific Bioscience (PacBio) Single Molecule Real-Time (SMRT) sequencing technology. A total of 18,524 unigenes were obtained, and 18,136 unigenes were successfully annotated. The raw data were uploaded to SRA database, and the BioProject ID is PRJNA650225. The above data will provide the basis for further exploration and understanding of the molecular mechanism in stress resistance or medicinal function of Apocynum venetum.

SUBMITTER: Zhang T

PROVIDER: S-EPMC7677113 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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Dataset of full-length transcriptome assembly and annotation of apocynum venetum using pacbio sequel II.

Zhang Tingting T Li Mao M Zhan Ya Guang YG Fan Gui Zhi GZ

Data in brief 20201104

Apocynum venetum, which belongs to Apocynaceae, is widely distributed throughout salt-barren zones, desert steppes, and alluvial flats of the Mediterranean area and Northwestern China. Apocynum venetum has long been used in traditional Chinese medicine because of its anti-inflammation, anti-oxidative, anti-hypertensive, anti-cancer, and bactericidal effects. However, the absence of genetic information on Apocynum venetum is an obstacle to understanding its stress resistance ...[more]

PMID: 33251304

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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

Dataset of full-length transcriptome assembly and annotation of apocynum venetum using pacbio sequel II.

Publications

Dataset of full-length transcriptome assembly and annotation of <i>apocynum venetum</i> using pacbio sequel II.

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