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Genome survey and SSR analysis of Apocynum venetum

Apocynum venetum is an eco-economic plant that exhibits high stress resistance. In the present paper, we carried out a whole-genome survey of A. venetum in order to provide a foundation for its whole-genome sequencing. High-throughput sequencing technology (Illumina NovaSep) was first used to measur...

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Autores principales: Li, Guo-qi, Song, Li-xiao, Jin, Chang-qing, Li, Miao, Gong, Shi-pei, Wang, Ya-fang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Portland Press Ltd. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6591564/
https://www.ncbi.nlm.nih.gov/pubmed/31189745
http://dx.doi.org/10.1042/BSR20190146
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author Li, Guo-qi
Song, Li-xiao
Jin, Chang-qing
Li, Miao
Gong, Shi-pei
Wang, Ya-fang
author_facet Li, Guo-qi
Song, Li-xiao
Jin, Chang-qing
Li, Miao
Gong, Shi-pei
Wang, Ya-fang
author_sort Li, Guo-qi
collection PubMed
description Apocynum venetum is an eco-economic plant that exhibits high stress resistance. In the present paper, we carried out a whole-genome survey of A. venetum in order to provide a foundation for its whole-genome sequencing. High-throughput sequencing technology (Illumina NovaSep) was first used to measure the genome size of A. venetum, and bioinformatics methods were employed for the evaluation of the genome size, heterozygosity ratio, repeated sequences, and GC content in order to provide a foundation for subsequent whole-genome sequencing. The sequencing analysis results indicated that the preliminary estimated genome size of A. venetum was 254.40 Mbp, and its heterozygosity ratio and percentage of repeated sequences were 0.63 and 40.87%, respectively, indicating that it has a complex genome. We used k-mer = 41 to carry out a preliminary assembly and obtained contig N50, which was 3841 bp with a total length of 223949699 bp. We carried out further assembly to obtain scaffold N50, which was 6196 bp with a total length of 227322054 bp. We performed simple sequence repeat (SSR) molecular marker prediction based on the A. venetum genome data and identified a total of 101918 SSRs. The differences between the different types of nucleotide repeats were large, with mononucleotide repeats being most numerous and hexanucleotide repeats being least numerous. We recommend the use of the ‘2+3’ (Illumina+PacBio) sequencing combination to supplement the Hi-C technique and resequencing technique in future whole-genome research in A. venetum.
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spelling pubmed-65915642019-06-27 Genome survey and SSR analysis of Apocynum venetum Li, Guo-qi Song, Li-xiao Jin, Chang-qing Li, Miao Gong, Shi-pei Wang, Ya-fang Biosci Rep Research Articles Apocynum venetum is an eco-economic plant that exhibits high stress resistance. In the present paper, we carried out a whole-genome survey of A. venetum in order to provide a foundation for its whole-genome sequencing. High-throughput sequencing technology (Illumina NovaSep) was first used to measure the genome size of A. venetum, and bioinformatics methods were employed for the evaluation of the genome size, heterozygosity ratio, repeated sequences, and GC content in order to provide a foundation for subsequent whole-genome sequencing. The sequencing analysis results indicated that the preliminary estimated genome size of A. venetum was 254.40 Mbp, and its heterozygosity ratio and percentage of repeated sequences were 0.63 and 40.87%, respectively, indicating that it has a complex genome. We used k-mer = 41 to carry out a preliminary assembly and obtained contig N50, which was 3841 bp with a total length of 223949699 bp. We carried out further assembly to obtain scaffold N50, which was 6196 bp with a total length of 227322054 bp. We performed simple sequence repeat (SSR) molecular marker prediction based on the A. venetum genome data and identified a total of 101918 SSRs. The differences between the different types of nucleotide repeats were large, with mononucleotide repeats being most numerous and hexanucleotide repeats being least numerous. We recommend the use of the ‘2+3’ (Illumina+PacBio) sequencing combination to supplement the Hi-C technique and resequencing technique in future whole-genome research in A. venetum. Portland Press Ltd. 2019-06-25 /pmc/articles/PMC6591564/ /pubmed/31189745 http://dx.doi.org/10.1042/BSR20190146 Text en © 2019 The Author(s). http://creativecommons.org/licenses/by/4.0/This is an open access article published by Portland Press Limited on behalf of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY) (http://creativecommons.org/licenses/by/4.0/) .
spellingShingle Research Articles
Li, Guo-qi
Song, Li-xiao
Jin, Chang-qing
Li, Miao
Gong, Shi-pei
Wang, Ya-fang
Genome survey and SSR analysis of Apocynum venetum
title Genome survey and SSR analysis of Apocynum venetum
title_full Genome survey and SSR analysis of Apocynum venetum
title_fullStr Genome survey and SSR analysis of Apocynum venetum
title_full_unstemmed Genome survey and SSR analysis of Apocynum venetum
title_short Genome survey and SSR analysis of Apocynum venetum
title_sort genome survey and ssr analysis of apocynum venetum
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6591564/
https://www.ncbi.nlm.nih.gov/pubmed/31189745
http://dx.doi.org/10.1042/BSR20190146
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