The complete chloroplast genome of the endangered species garra de león [Bomarea ovallei (Phil.) Ravenna] from Chile

IF 1 4区生物学 Q3 PLANT SCIENCES

Indian Journal of Genetics and Plant Breeding Pub Date : 2022-09-30 DOI:10.31742/isgpb.82.3.14

R. Diaz, W. H. Mamani, Liesbeth van den Brink, Maria N. Fuentes, M. A. Aburto

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Abstract

Bomarea ovallei (Phil.) Ravenna (2n=2x=18) is an endangered endemic species that inhabits only a small part of the coast of the Atacama region. We describe the structure, gene composition and phylogeny of the complete chloroplast sequence of this elusive species. The chloroplast genome consists of 155,018 bp, with typical quadripartite structures: a large single copy region (LSC) of 84,132 bp, a small single copy region (SSC) of 17,794 bp, and two inverted repeat regions (IRs) contain 26,546 bp. One hundred and thirty-four genes were identified out of which 84 coding genes, 8 rRNA, 38 tRNA and 4 pseudogenes. B. ovallei chloroplast resembles chloroplasts from seven species of the order Liliales in length and structure and is most similar to Bomarea edulis (BP=100). The average nucleotide variability (Pi) of 0.00254 between these two Bomarea species is moderate. Nine loci with increased variability were identified: rps16-trnQ, atpF, trnL, ndhC-trnV, rbcL, psbJ, rpl32-trnL, ndhD and ycf1. These loci could be used as DNA markers for classification and evaluation studies in Bomarea populations.

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智利濒危物种garra de león[Bomarea ovallei（Phil.）Ravenna]的完整叶绿体基因组

蛋形区(菲尔)拉文纳(2n=2x=18)是一种濒临灭绝的地方性物种，仅栖息在阿塔卡马地区海岸的一小部分地区。我们描述了这个难以捉摸的物种的完整叶绿体序列的结构，基因组成和系统发育。叶绿体基因组全长155,018 bp，具有典型的四部结构:大单拷贝区(LSC)长度为84,132 bp，小单拷贝区(SSC)长度为17,794 bp，两个反向重复区(IRs)长度为26,546 bp。共鉴定出134个基因，其中编码基因84个，rRNA 8个，tRNA 38个，假基因4个。卵形叶的叶绿体在长度和结构上与百合目7种植物的叶绿体相似，与Bomarea edulis最相似(BP=100)。平均核苷酸变异率(Pi)为0.00254，为中等。鉴定出9个变异增加的位点:rps16-trnQ、atpF、trnL、ndhC-trnV、rbcL、psbJ、rpl32-trnL、ndhD和ycf1。这些基因座可作为Bomarea群体分类和评价研究的DNA标记。

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来源期刊

Indian Journal of Genetics and Plant Breeding PLANT SCIENCES-

CiteScore

1.80

自引率

10.00%

发文量

审稿时长

6-12 weeks

期刊介绍： Advance the cause of genetics and plant breeding and to encourage and promote study and research in these disciplines in the service of agriculture; to disseminate the knowledge of genetics and plant breeding; provide facilities for association and conference among students of genetics and plant breeding and for encouragement of close relationship between them and those in the related sciences; advocate policies in the interest of the nation in the field of genetics and plant breeding, and facilitate international cooperation in the field of genetics and plant breeding.