Characterization of the complete chloroplast genome sequence of Cardamine macrophylla (Brassicaceae)

被引：4

作者：

Ren, Ting ^{[1
]}

Yang, Yanci ^{[1
]}

Wang, Jiao ^{[1
]}

Zhang, Ruiting ^{[1
]}

Liu, Zhan-Lin ^{[1
]}

机构：

[1] Northwest Univ, Coll Life Sci, Minist Educ, Key Lab Resource Biol & Biotechnol Western China, Xian 710069, Shaanxi, Peoples R China

来源：

CONSERVATION GENETICS RESOURCES | 2018年 / 10卷 / 04期

基金：

中国国家自然科学基金;

关键词：

Cardamine macrophylla; Plastome; Illumina sequencing; Phylogenetic analysis;

D O I：

10.1007/s12686-017-0880-4

中图分类号：

X176 [生物多样性保护];

学科分类号：

090705 ;

摘要：

Cardamine macrophylla is a perennial herb with short-lived seeds. Here, the complete chloroplast genome (plastome) of C.macrophylla was obtained by Illumina sequencing technology. The plastome is 155,393 bp in length, including a large single copy (LSC) region of 84,492 bp, a small single copy (SSC) region of 17,957 bp and a pair of inverted repeats (IRs) of 26,472 bp. The genome contained 131 genes, including 85 protein-coding genes (78 PCG species), 37 tRNA genes (30 tRNA species), eight rRNA genes (four rRNA species) and one pseudogene. Among these genes, 15 genes harbored a single intron and three genes harbored two introns. Seven tRNA, five protein-coding and all four rRNA genes were completely duplicated in the IR regions. The GC content of C. macrophylla plastome is 36.4%. A total of 26,470 codons were detected in 85 protein-coding genes of C. macrophylla plastome. Phylogenetic analysis demonstrated that the all Cardamine species formed a monophyletic clade, and C. macrophylla was closely related to C. impatiens.

引用

页码：627 / 630

页数：4

共 10 条

[1] Accelerated modern human-induced species losses: Entering the sixth mass extinction [J].

Ceballos, Gerardo ;

Ehrlich, Paul R. ;

Barnosky, Anthony D. ;

Garcia, Andres ;

Pringle, Robert M. ;

Palmer, Todd M. .

SCIENCE ADVANCES, 2015, 1 (05)

[2] Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs [J].

Chevreux, B ;

Pfisterer, T ;

Drescher, B ;

Driesel, AJ ;

Müller, WEG ;

Wetter, T ;

Suhai, S .

GENOME RESEARCH, 2004, 14 (06) :1147-1159

[3] Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads-a baiting and iterative mapping approach [J].

Hahn, Christoph ;

Bachmann, Lutz ;

Chevreux, Bastien .

NUCLEIC ACIDS RESEARCH, 2013, 41 (13) :e129

[4]

Li SL, 2010, RESOUR DEV MARKET, V26, P139

[5] OrganellarGenomeDRAW-a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets [J].

Lohse, Marc ;

Drechsel, Oliver ;

Kahlau, Sabine ;

Bock, Ralph .

NUCLEIC ACIDS RESEARCH, 2013, 41 (W1) :W575-W581

[6] NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data [J].

Patel, Ravi K. ;

Jain, Mukesh .

PLOS ONE, 2012, 7 (02)

[7] THE CODON ADAPTATION INDEX - A MEASURE OF DIRECTIONAL SYNONYMOUS CODON USAGE BIAS, AND ITS POTENTIAL APPLICATIONS [J].

SHARP, PM ;

LI, WH .

NUCLEIC ACIDS RESEARCH, 1987, 15 (03) :1281-1295

[8] RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models [J].

Stamatakis, Alexandros .

BIOINFORMATICS, 2006, 22 (21) :2688-2690

[9] Extinction risk from climate change [J].

Thomas, CD ;

Cameron, A ;

Green, RE ;

Bakkenes, M ;

Beaumont, LJ ;

Collingham, YC ;

Erasmus, BFN ;

de Siqueira, MF ;

Grainger, A ;

Hannah, L ;

Hughes, L ;

Huntley, B ;

van Jaarsveld, AS ;

Midgley, GF ;

Miles, L ;

Ortega-Huerta, MA ;

Peterson, AT ;

Phillips, OL ;

Williams, SE .

NATURE, 2004, 427 (6970) :145-148

[10]

[张宇 ZHANG Yu], 2006, [植物生理学通讯, Plant Physiology Communications], V42, P256

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