The complete chloroplast genome sequence of Rubus hirsutus Thunb. and a comparative analysis within Rubus species.

IF 1.3 4区生物学 Q4 GENETICS & HEREDITY

Genetica Pub Date : 2021-12-01 Epub Date: 2021-09-21 DOI:10.1007/s10709-021-00131-9

Qirui Wang, Ziru Huang, Chenshu Gao, Yuqing Ge, Rubin Cheng

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引用次数: 5

Abstract

Rubus hirsutus is a type of tonifying kidney-essence herb that belongs to the Rosaceae family, and has been commonly used to treat multiple diseases, such as polyuria, impotence, and infertility. In this study, we determined the complete chloroplast sequence of R. hirsutus and conduced a comparative analysis within the genus Rubus. The assembled chloroplast (cp.) genome is 156,380 bp in length with a GC content of 37.0% and shares a conserved quadripartite structure within the other cp. genomes in this genus. A total of 132 unique genes were annotated in the cp. genome of R. hirsutus, which contained 87 protein-coding genes, 37 tRNAs, and eight rRNAs. Seventeen duplicated genes were identified in the inverted repeats region. Furthermore, 70 simple sequence repeats and 35 long repeats were detected in total in the R. hirsutus chloroplast genome. Eight mutational hotspots were identified in the cp. genome of this species with higher nucleotide variations in non-coding regions than those of coding regions. Furthermore, the gene order, codon usage, and repeat sequence distribution were highly consistent in Rubus according to the results of a comparative analysis. A phylogenetic analysis indicated that there was a sister relationship between R. hirsutus and R. chingii. Overall, the complete chloroplast genome of R. hirsutus and the comparative analysis will help to further the evolutionary study, conservation, phylogenetic reconstruction, and development of molecular barcodes for the genus Rubus.

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毛茛叶绿体全基因组序列。以及种间的比较分析。

毛蕊草是蔷薇科的一种补肾精草本植物，常用于治疗多种疾病，如多尿症、阳痿和不育症。在本研究中，我们测定了红毛猴属植物的完整叶绿体序列，并对红毛猴属植物进行了比较分析。组装后的叶绿体基因组全长156,380 bp, GC含量为37.0%，与该属其他叶绿体基因组具有保守的四分体结构。在毛猴cp.基因组中共标注了132个独特基因，其中包含87个蛋白编码基因、37个trna和8个rnas。在反向重复序列区鉴定出17个重复基因。在毛猴叶绿体基因组中共检测到70个简单重复序列和35个长重复序列。在该物种的cp.基因组中发现了8个突变热点，非编码区的核苷酸变异高于编码区的核苷酸变异。此外，比较分析结果表明，在基因顺序、密码子使用和重复序列分布方面，红毛猴具有高度的一致性。系统发育分析表明，毛鼠与中华毛鼠存在亲缘关系。综上所述，毛猴属植物叶绿体全基因组的研究和比较分析将有助于进一步研究毛猴属植物的进化、保护、系统发育重建和分子条形码的开发。

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来源期刊

Genetica 生物-遗传学

CiteScore

2.70

自引率

0.00%

发文量

审稿时长

>12 weeks

期刊介绍： Genetica publishes papers dealing with genetics, genomics, and evolution. Our journal covers novel advances in the fields of genomics, conservation genetics, genotype-phenotype interactions, evo-devo, population and quantitative genetics, and biodiversity. Genetica publishes original research articles addressing novel conceptual, experimental, and theoretical issues in these areas, whatever the taxon considered. Biomedical papers and papers on breeding animal and plant genetics are not within the scope of Genetica, unless framed in an evolutionary context. Recent advances in genetics, genomics and evolution are also published in thematic issues and synthesis papers published by experts in the field.