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韭菜(石蒜科)完整叶绿体基因组的特征分析

Characterization of the complete chloroplast genome of leek L. (Amaryllidaceae).

作者信息

Filyushin Mikhail A, Beletsky Alexey V, Kochieva Elena Z

机构信息

Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.

出版信息

Mitochondrial DNA B Resour. 2019 Jul 22;4(2):2602-2603. doi: 10.1080/23802359.2019.1640090.

DOI:10.1080/23802359.2019.1640090
PMID:33365644
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7706495/
Abstract

The complete chloroplast genome sequence of was determined by Illumina single-end sequencing. The complete plastid genome was 152,732 bp in length containing a large single copy (LSC) of 81,744 bp and a small single copy (SSC) of 17,910 bp, which were separated by a pair of 26,524 bp inverted repeats (IRs). A total of 133 genes were annotated, including 80 protein-coding genes, 38 tRNA genes, 8 rRNA genes, and 7 pseudogenes. The overall GC contents of the plastid genome were 36.7%. Unlike and in the leek, plastome gene is absent, and gene is a pseudogene due to a 4 bp deletion and the formation of a premature stop codon.

摘要

通过Illumina单端测序确定了[物种名称]的完整叶绿体基因组序列。完整的质体基因组长度为152,732 bp,包含一个81,744 bp的大单拷贝(LSC)和一个17,910 bp的小单拷贝(SSC),它们被一对26,524 bp的反向重复序列(IRs)隔开。总共注释了133个基因,包括80个蛋白质编码基因、38个tRNA基因、8个rRNA基因和7个假基因。质体基因组的总体GC含量为36.7%。与韭菜中的[其他物种名称1]和[其他物种名称2]不同,质体基因组中不存在[基因名称1]基因,并且[基因名称2]基因由于4 bp的缺失和过早终止密码子的形成而成为假基因。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6c0f/7706495/f8f2e37f5008/TMDN_A_1640090_F0001_B.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6c0f/7706495/f8f2e37f5008/TMDN_A_1640090_F0001_B.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6c0f/7706495/f8f2e37f5008/TMDN_A_1640090_F0001_B.jpg

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本文引用的文献

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2
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Mitochondrial DNA B Resour. 2016 Nov 12;1(1):831-832. doi: 10.1080/23802359.2016.1247669.
3
Bandage: interactive visualization of de novo genome assemblies.绷带:从头基因组组装的交互式可视化
Bioinformatics. 2015 Oct 15;31(20):3350-2. doi: 10.1093/bioinformatics/btv383. Epub 2015 Jun 22.
4
Metabolite profiling of leek (Allium porrum L) cultivars by (1) H NMR and HPLC-MS.利用¹H NMR和HPLC-MS对韭菜(葱属植物韭葱)品种进行代谢物谱分析。
Phytochem Anal. 2014 May-Jun;25(3):220-8. doi: 10.1002/pca.2495. Epub 2014 Jan 10.
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.