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Comparative analysis of complete chloroplast genome sequences of four major Amorphophallus species.
Scientific Reports ( IF 3.8 ) Pub Date : 2019-01-28 , DOI: 10.1038/s41598-018-37456-z
Erxi Liu 1, 2 , Chaozhu Yang 2 , Jiangdong Liu 1 , Surong Jin 3 , Nunung Harijati 4 , Zhongli Hu 1 , Ying Diao 1 , Lingling Zhao 1
Affiliation  

Amorphophallus (Araceae) contains more than 170 species that are mainly distributed in Asia and Africa. Because the bulbs of Amorphophallus are rich in glucomannan, they have been widely used in food, medicine, the chemical industry and so on. To better understand the evolutionary relationships and mutation patterns in the chloroplast genome of Amorphophallus, the complete chloroplast genomes of four species were sequenced. The chloroplast genome sequences of A. albus, A. bulbifer, A. konjac and A. muelleri ranged from 162,853 bp to 167,424 bp. The A. albus chloroplast (cp) genome contains 113 genes, including 79 protein-coding genes, 30 tRNA genes and 4 rRNA genes. The A. bulbifer cp genome contains 111 genes, including 78 protein-coding genes, 29 tRNA genes and 4 rRNA genes. A. muelleri contains 111 and 113 genes, comprising 78 and 80 protein-coding genes, respectively, 29 tRNA genes and 4 rRNA genes. The IR (inverted repeat) region/LSC (long single copy) region and IR/SSC (short single copy) region borders of the four Amorphophallus cp genomes were compared. In addition to some genes being deleted, variations in the copy numbers and intron numbers existed in some genes in the four cp genomes. One hundred thirty-four to 164 SSRs (simple sequence repeats) were detected in the four cp genomes. In addition, the highest mononucleotide SSRs were composed of A and T repeat units, and the majority of dinucleotides were composed of AT and TA. SNPs (single nucleotide polymorphisms) and indels (insertion-deletions) were calculated from coding genes and noncoding genes, respectively. These divergences comprising SSRs, SNPs and indel markers will be useful in testing the maternal inheritance of the chloroplast genome, identifying species differentiation and even in breeding programs. Furthermore, the regression of ndhK was detected from four Amorphophallus cp genomes in our study. Complete cp genome sequences of four Amorphophallus species and other plants were used to perform phylogenetic analyses. The results showed that Amorphophallus was clustered in Araceae, and Amorphophallus was divided into two clades; A. albus and A. konjac were clustered in one clade, and A. bulbifer and A. muelleri were clustered in another clade. Phylogenetic analysis among the Amorphophallus genus was conducted based on matK and rbcL. The phylogenetic trees showed that the relationships among the Amorphophallus species were consistent with their geographical locations. The complete chloroplast genome sequence information for the four Amorphophallus species will be helpful for elucidating Amorphophallus phylogenetic relationships.



中文翻译:

四种主要魔芋属物种完整叶绿体基因组序列的比较分析。

魔芋(Araceae)包含170多个物种,主要分布在亚洲和非洲。由于魔芋的球茎富含葡甘露聚糖,因此已被广泛用于食品,医药,化学工业等。为了更好地了解魔芋叶绿体基因组中的进化关系和突变模式,对四个物种的完整叶绿体基因组进行了测序。的叶绿体基因组序列黄鳝一个bulbifer魔芋一个muelleri的范围为162,853 bp至167,424 bp。在一个Albus叶绿体(cp)基因组包含113个基因,其中包括79个蛋白质编码基因,30个tRNA基因和4个rRNA基因。的一个鳞茎cp基因组包含111个基因,其中包括78个蛋白质编码基因,29个tRNA基因和4个rRNA基因。muelleri包含111和113个基因,分别包含78和80个蛋白质编码基因,29个tRNA基因和4个rRNA基因。四个魔芋的IR(反向重复)区域/ LSC(长单拷贝)区域和IR / SSC(短单拷贝)区域边界比较了cp基因组。除了删除某些基因外,四个cp基因组中的某些基因还存在拷贝数和内含子数的变异。在四个cp基因组中检测到了一百三十四到164个SSR(简单的序列重复)。另外,最高的单核苷酸SSR由A和T重复单元组成,而大多数二核苷酸由AT和TA组成。分别从编码基因和非编码基因计算出SNP(单核苷酸多态性)和插入缺失(插入缺失)。这些由SSR,SNP和indel标记组成的差异将对测试叶绿体基因组的母本遗传,鉴定物种分化甚至在育种程序中很有用。此外,从四个方面检测到ndhK的回归我们研究中的魔芋cp基因组。使用四种魔芋属植物和其他植物的完整cp基因组序列进行系统发育分析。结果表明,魔芋聚集在天南星科中魔芋分为两个进化枝。黄鳝一个魔芋聚集在一个分支中,而A则聚集在一个分支中。bulbifer一个穆勒里聚集在另一个分支中。基于matK进行了魔芋属的系统发育分析rbcL。系统发育树表明,魔芋物种之间的关系与其地理位置是一致的。四个魔芋物种的完整叶绿体基因组序列信息将有助于阐明魔芋的系统发生关系。

更新日期:2019-01-28
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