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一种极度濒危兰花物种(兰科)的完整叶绿体基因组序列

The complete chloroplast genome sequences of a highly Endangered orchid species (Orchidaceae).

作者信息

Li Mingyu, Zhao Zhe, He Jian, Cheng Jin, Xie Lei

机构信息

Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.

School of Nature Conservation, Beijing Forestry University, Beijing, China.

出版信息

Mitochondrial DNA B Resour. 2019 Sep 5;4(2):2928-2929. doi: 10.1080/23802359.2019.1660269.

DOI:10.1080/23802359.2019.1660269
PMID:33365796
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7706826/
Abstract

(Orchidaceae) is an endangered species with highly ornamental and horticultural value. The chloroplast genome of the species was assembled using next-generation sequencing method. The complete cp genome sequence is 156,329 bp in length, comprising a pair of inverted repeat regions (IRs) of 34,214 bp each, separated by a large single-copy (LSC) region of 86056 bp, and a small single-copy (SSC) region of 1845 bp. The chloroplast genome contains 126 functional genes, including 80 protein-coding genes (PCGs), 38 tRNA genes, and 8 rRNA genes. The phylogenetic position of the species based on the complete cp genome was also inferred in this study.

摘要

(兰科)是一种具有高度观赏和园艺价值的濒危物种。该物种的叶绿体基因组采用下一代测序方法进行组装。完整的叶绿体基因组序列长度为156,329 bp,包括一对长度均为34,214 bp的反向重复区域(IRs),被一个86,056 bp的大单拷贝(LSC)区域和一个1,845 bp的小单拷贝(SSC)区域隔开。叶绿体基因组包含126个功能基因,包括80个蛋白质编码基因(PCGs)、38个tRNA基因和8个rRNA基因。本研究还基于完整的叶绿体基因组推断了该物种的系统发育位置。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d625/7706826/c1d9d1436b8a/TMDN_A_1660269_F0001_B.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d625/7706826/c1d9d1436b8a/TMDN_A_1660269_F0001_B.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d625/7706826/c1d9d1436b8a/TMDN_A_1660269_F0001_B.jpg

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引用本文的文献

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In-depth analysis of genomes and functional genomics of orchid using cutting-edge high-throughput sequencing.利用前沿的高通量测序技术对兰花基因组和功能基因组进行深入分析。
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本文引用的文献

1
Seven New Complete Plastome Sequences Reveal Rampant Independent Loss of the ndh Gene Family across Orchids and Associated Instability of the Inverted Repeat/Small Single-Copy Region Boundaries.七个新的完整质体基因组序列揭示了兰花中ndh基因家族的大量独立丢失以及反向重复/小单拷贝区域边界的相关不稳定性。
PLoS One. 2015 Nov 11;10(11):e0142215. doi: 10.1371/journal.pone.0142215. eCollection 2015.
2
Plann: A command-line application for annotating plastome sequences.Plann:一个用于注释质体基因组序列的命令行应用程序。
Appl Plant Sci. 2015 Aug 10;3(8). doi: 10.3732/apps.1500026. eCollection 2015 Aug.
3
The location and translocation of ndh genes of chloroplast origin in the Orchidaceae family.
兰科植物中叶绿体来源的ndh基因的定位与易位
Sci Rep. 2015 Mar 12;5:9040. doi: 10.1038/srep09040.
4
Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.Geneious Basic:一个集成和可扩展的桌面软件平台,用于组织和分析序列数据。
Bioinformatics. 2012 Jun 15;28(12):1647-9. doi: 10.1093/bioinformatics/bts199. Epub 2012 Apr 27.
5
Pollination by deceit in Paphiopedilum barbigerum (Orchidaceae): a staminode exploits the innate colour preferences of hoverflies (Syrphidae).髯毛兜兰(兰科)的欺骗性传粉:一个退化雄蕊利用了食蚜蝇(食蚜蝇科)天生的颜色偏好。
Plant Biol (Stuttg). 2009 Jan;11(1):17-28. doi: 10.1111/j.1438-8677.2008.00120.x.