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珀金斯安息香属(安息香科)的完整叶绿体基因组。

The complete chloroplast genome of Perkins (Styracaceae).

作者信息

Xu Xiaogang, Zhang Yaoqin, Tong Lili, Wang Yabo, Xia Chongli

机构信息

Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China.

State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanping, China.

出版信息

Mitochondrial DNA B Resour. 2020 Jan 31;5(1):961-962. doi: 10.1080/23802359.2020.1721375.

DOI:10.1080/23802359.2020.1721375
PMID:33366827
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7748644/
Abstract

In this work, next-generation sequencing was applied to measure the complete chloroplast genome of for the sake of offering valuable genomic information to promote its conservation. The complete chloroplast genome sequence of was measured as 157,501 bp in size. It contains the typical structure and gene content of angiosperm plastome, which includes a large single-copy (LSC), a small single-copy (SSC), and 2 inverted repeat (IR) regions of 87,130 bp, 18,277 bp, and 26,047 bp, respectively. The chloroplast genome has a total of 130 genes including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Overall, GC contents of the genome were 36.96%. Phylogenetic analysis based on the 29 chloroplast genome measurement demonstrated that is most closely related to Griff.

摘要

在这项工作中,为了提供有价值的基因组信息以促进其保护,应用了下一代测序技术来测定[物种名称]的完整叶绿体基因组。[物种名称]的完整叶绿体基因组序列测定大小为157,501 bp。它包含被子植物质体基因组的典型结构和基因内容,其中包括一个大单拷贝(LSC)、一个小单拷贝(SSC)以及两个分别为87,130 bp、18,277 bp和26,047 bp的反向重复(IR)区域。[物种名称]的叶绿体基因组共有130个基因,包括85个蛋白质编码基因、37个tRNA基因和8个rRNA基因。总体而言,该基因组的GC含量为36.96%。基于29个叶绿体基因组测定的系统发育分析表明,[物种名称]与[物种名称]Griff.关系最为密切。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c84a/7748644/1323e1ad0738/TMDN_A_1721375_F0001_B.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c84a/7748644/1323e1ad0738/TMDN_A_1721375_F0001_B.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c84a/7748644/1323e1ad0738/TMDN_A_1721375_F0001_B.jpg

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本文引用的文献

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Comparative analysis of complete chloroplast genome sequence and inversion variation in Lasthenia burkei (Madieae, Asteraceae).伯克氏拉氏菊(菊科,母菊族)叶绿体全基因组序列及倒位变异的比较分析
Am J Bot. 2014 Apr;101(4):722-9. doi: 10.3732/ajb.1400049. Epub 2014 Apr 3.
2
Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements, repeats, and nucleotide substitution rates.石竹目植物祖先质体基因组的重建揭示了基因组重排、重复序列和核苷酸替换率之间的相关性。
Mol Biol Evol. 2014 Mar;31(3):645-59. doi: 10.1093/molbev/mst257. Epub 2013 Dec 12.
3
MAFFT multiple sequence alignment software version 7: improvements in performance and usability.
MAFFT 多序列比对软件版本 7:性能和易用性的改进。
Mol Biol Evol. 2013 Apr;30(4):772-80. doi: 10.1093/molbev/mst010. Epub 2013 Jan 16.
4
CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences.CpGAVAS,一个整合的网络服务器,用于完全测序的叶绿体基因组序列的注释、可视化、分析和 GenBank 提交。
BMC Genomics. 2012 Dec 20;13:715. doi: 10.1186/1471-2164-13-715.
5
SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.SPAdes:一种新的基因组组装算法及其在单细胞测序中的应用
J Comput Biol. 2012 May;19(5):455-77. doi: 10.1089/cmb.2012.0021. Epub 2012 Apr 16.