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The chloroplast genome sequence of the green macroalga Caulerpa okamurae (Ulvophyceae, Chlorophyta): Its structural features, organization and phylogenetic analysis
Marine Genomics ( IF 1.3 ) Pub Date : 2020-02-01 , DOI: 10.1016/j.margen.2020.100752
Fengrong Zheng , Bo Wang , Zhen Shen , Zongxing Wang , Wei Wang , Hongzhan Liu , Claire Wang , Maosheng Xin

To clarify evolutionary characteristics, phylogenetic relationships as well as species identification of C. okamurae, we determined the cpDNA sequence of Caulerpa okamurae using de novo sequencing in the present study. The cpDNA of C. okamurae was 148,274 bp in length, and it lacked the inverted repeat commonly found in vascular green plants. The cpDNA of C. okamurae was highly compact with a gene density of 71.7%. Moreover, it was an AT-rich genome (65.5%) consisting 76 protein-coding genes (PCGs), 27 transfer RNA (tRNA) genes, three ribosomal RNA (rRNA) genes, 32 putative open reading frames (ORFs) and six introns. Additionally, the six introns were annotated in six genes as follows: psbA, rpoB, ftsH, psbD, atpF and cysA. The overall base composition of its cpDNA was 65.46% for AT. A total of 56 genes were encoded on the light strand, while all the other 50 chloroplast genes were encoded on the heavy strand. All of the PCGs had ATG as their start codon and employed TAA, TGA or TAG as their termination codon. Phylogenetic analyses suggested that the complete cpDNA sequence of C. okamurae fell in the Chlorophyta, Ulvophyceae, Bryopsidales, and Caulerpaceae and more resembled the cpDNAs of C. racemosa, C. cliftonii voucher and Tydemania expeditionis. Taken together, our data offered useful information for the studies of C.okamurae on evolutionary characteristics, phylogenetic relationships as well as species identification.



中文翻译:

绿巨藻(Culerpa okamurae)(Ulvophyceae,Chlorophyta)的叶绿体基因组序列:其结构特征,组织和系统发育分析

为了弄清冈村衣藻的进化特征,系统发育关系以及物种鉴定,我们在本研究中使用从头测序法确定了冈村猫的cpDNA序列。冈村梭菌的cpDNA长度为148,274 bp,缺乏在维管植物中常见的反向重复序列。冈村梭菌的cpDNA高度紧凑,基因密度为71.7%。此外,它是一个富含AT的基因组(65.5%),由76个蛋白质编码基因(PCG),27个转移RNA(tRNA)基因,三个核糖体RNA(rRNA)基因,32个推定开放阅读框(ORF)和六个内含子组成。另外,六个内含子在六个基因中注释如下:psbA,rpoB,ftsH,psbD,atpF和cysA。对于AT,其cpDNA的总体碱基组成为65.46%。轻链上总共编码了56个基因,而其余50个叶绿体基因全部编码在了重链上。所有PCG均以ATG为起始密码子,并以TAA,TGA或TAG为终止密码子。系统发育分析表明,冈氏梭菌的完整cpDNA序列落在叶绿藻,叶藻科,苔藓科和菜豆科中,并且更类似于消旋衣藻,C。cliftonii凭证Tydemania expeditionis的cpDNA。两者合计,我们的数据提供了有用的信息,为研究冈形衣藻的进化特征,系统发育关系以及物种鉴定提供了有用的信息。

更新日期:2020-02-01
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