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Comparative analysis of the complete chloroplast genome sequences of three Amaranthus species

Published online by Cambridge University Press:  24 January 2019

Su-Young Hong ,
Kyeong-Sik Cheon ,
Ki-Oug Yoo ,
Hyun-Oh Lee ,
Manjulatha Mekapogu  and
Kwang-Soo Cho
Su-Young Hong
Affiliation:
Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
Kyeong-Sik Cheon
Affiliation:
Department of Biological Science, Sangji University, Wonju, Republic of Korea
Ki-Oug Yoo
Affiliation:
Department of Biology, Kangwon National University, Chuncheon, Republic of Korea
Hyun-Oh Lee
Affiliation:
Phygen Genomics Institute, Baekgoong Plaza 1, Bundang-gu, Seongnam, Republic of Korea
Manjulatha Mekapogu
Affiliation:
Floriculture Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Wanju 55365, Republic of Korea
Kwang-Soo Cho*
Affiliation:
Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea
*
*Corresponding author. E-mail: kscholove@korea.kr
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Abstract

The complete chloroplast (cp) genome sequences of three Amaranthus species (Amaranthus hypochondriacus, A. cruentus and A. caudatus) were determined by next-generation sequencing. The cp genome sequences of A. hypochondriacus, A. cruentus and A. caudatus were 150,523, 150,757 and 150,523 bp in length, respectively, each containing 84 genes with identical contents and orders. Expansion or contraction of the inverted repeat region was not observed among the three Amaranthus species. The coding regions were highly conserved with 99.3% homology in nucleotide and amino acid sequences. Five genes – matK, accD, ndhJ, ccsA and ndhF – showed relatively high non-synonymous/synonymous values (Ka/Ks > 0.1). Sequence comparison identified two insertion/deletion (InDels) greater than 40 bp in length, and polymerase chain reaction markers that could amplify these InDel regions were applied to diverse Korean Genbank accessions, which could discriminate the three Amaranthus species. Phylogenetic analyses based on 62 protein-coding genes showed that the core Caryophyllales were monophyletic and Amaranthoideae formed a sister group with the Betoideae and Chenopodioideae clade. Comparing each homologous locus among the three Amaranthus species, identified eight regions with high Pi values (>0.03). Seven of these loci, except for rps19-trnH (GUG), were considered to be useful molecular markers for further phylogenetic studies.

Keywords

Amaranthuschloroplast genomeInDelphylogenetic analysistandem repeats
Type
Research Article
Information
Plant Genetic Resources , Volume 17 , Issue 3 , June 2019 , pp. 245 - 254
Copyright
Copyright © NIAB 2019 

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Footnotes

†

These authors contributed equally to this work.

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