Wu Zhiqiang
a Department of Biology , Colorado State University , Fort Collins , CO , USA.
Mitochondrial DNA A DNA Mapp Seq Anal. 2016 Jul;27(4):2561-2. doi: 10.3109/19401736.2015.1038804. Epub 2015 May 29.
The whole nucleotide sequence of the chloroplast genome from Capsella rubella is determined in this study using short Illumina sequence data from public database. The circular double-stranded DNA, which consists of 154,601 base pairs (bp) in size, contains a pair of inverted repeats (IRa and IRb) of 26,462 bp each, which are separated by a small and large single-copies (SSC and LSC) of 17,855 and 83,822 bp, respectively. The overall GC content of the chloroplast genome is 36.54% and the GC contents of LSC, IRs and SSC are 34.33%, 42.38% and 29.61% separately. One hundred and twelve unique genes were annotated, including 78 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Among these, 16 are duplicated in the inverted repeat regions, 15 genes contained 1 intron, and 3 genes (rps12, clpP and ycf3) comprised of 2 introns. Two protein genes (rps19 and ycf1) span in the boundaries of LSC-IR and IR-SSC to produce two partial pseudogenes.
本研究利用来自公共数据库的短读长Illumina序列数据，测定了风花菜叶绿体基因组的全核苷酸序列。该环状双链DNA大小为154,601碱基对（bp），包含一对大小均为26,462 bp的反向重复序列（IRa和IRb），它们被大小分别为17,855 bp和83,822 bp的一个小单拷贝区（SSC）和一个大单拷贝区（LSC）隔开。叶绿体基因组的总体GC含量为36.54%，LSC、IR和SSC的GC含量分别为34.33%、42.38%和29.61%。共注释了112个独特基因，包括78个蛋白质编码基因、30个tRNA基因和4个rRNA基因。其中，16个基因在反向重复区域中重复，15个基因含有1个内含子，3个基因（rps12、clpP和ycf3）含有2个内含子。两个蛋白质基因（rps19和ycf1）跨越LSC-IR和IR-SSC边界，产生两个部分假基因。
