Hostname: page-component-76fb5796d-x4r87 Total loading time: 0 Render date: 2024-04-25T17:16:51.835Z Has data issue: false hasContentIssue false
  • English
  • Français

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
Get access Rights & Permissions [Opens in a new window]

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 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

Footnotes

†

These authors contributed equally to this work.

References

Aaron, SF, Daniel, ZS, Al-Khatib, K and Michael, JH (2001) Pollen morphological differences in Amaranthus Species and interspecific hybrids. Weed Science 49: 732–737.Google Scholar
Adhikary, D and Pratt, DB (2015) Morphologic and taxonomic analysis of the weedy and cultivated Amaranthus hybridus Species Complex. Systematic Botany 40: 604–610.Google Scholar
Benson, G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research 27: 573–580.Google Scholar
Birky, CW Jr (2001) The inheritance of genes in mitochondria and chloroplasts: laws, mechanisms, and models. Annual Review of Genetics 35: 125–148.Google Scholar
Chaney, L, Mangelson, R, Ramaraj, T, Jellen, EN and Maughan, PJ (2016) The complete chloroplast genome sequences for four Amaranthus species (Amaranthaceae). Applications in Plant Sciences 4: apps.1600063.Google Scholar
Cheon, K-S, Kim, K-A and Yoo, K-O (2017) The complete chloroplast genome sequences of three Adenophora species and comparative analysis with Campanuloid species (Campanulaceae). PLoS ONE 12: e0183652.Google Scholar
Cho, K-S, Cheon, K-S, Hong, S-Y, Cho, J-H, Im, J-S, Mekapogu, M, Yu, Y-S and Park, T-H (2016) Complete chloroplast genome sequences of Solanum commersonii and its application to chloroplast genotype in somatic hybrids with Solanum tuberosum. Plant Cell Reports 35: 2113–2123.Google Scholar
Cho, K-S, Hong, S-Y, Yun, B-K, Won, H-S, Yoon, Y-H, Kwon, K-B and Mekapogu, M (2017) Application of InDel markers based on the chloroplast genome sequence for authentication and traceability of Tartary and common buckwheat. Czech Journal of Food Sciences 35: 122–130.Google Scholar
Cho, K-S, Yun, B-K, Yoon, Y-H, Hong, S-Y, Mekapogu, M, Kim, K-H and Yang, T-J (2015) Complete chloroplast genome sequence of Tartary buckwheat (Fagopyrum tataricum) and comparative analysis with common buckwheat (F. esculentum). PLoS ONE 10: e0125332.Google Scholar
Costea, M and DeMason, DA (2001) Stem morphology and anatomy in Amaranthus l. (Amaranthaceae), taxonomic significance. The Journal of the Torrey Botanical Society 128: 254–281.Google Scholar
Cuenoud, P, Savolainen, V, Chatrou, LW, Powell, M, Grayer, RJ and Chase, MW (2002) Molecular phylogenetics of Caryophyllales based on nuclear 18S rDNA and plastid rbcL, atpB, and matK DNA sequences. American Journal of Botany 89: 132–144.Google Scholar
Darriba, D, Taboada, GL, Doallo, R and Posada, D (2012) Jmodeltest 2: more models, new heuristics and parallel computing. Nature Methods 9: 772.Google Scholar
Das, S (2016) Taxonomy and phylogeny of grain amaranths. In: Amaranthus: A Promising Crop of Future. Singapore: Springer Singapore, pp. 57–94. doi: 10.1007/978-981-10-1469-7_5.Google Scholar
Dong, W, Liu, J, Yu, J, Wang, L and Zhou, S (2012) Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding. PLoS ONE 7: e35071.Google Scholar
El-Ghamery, AA, Sadek, AM and Abd Elbar, OH (2015) Root anatomy of some species of Amaranthus (amaranthaceae) and formation of successive cambia. Annals of Agricultural Sciences 60: 53–60.Google Scholar
Frazer, KA, Pachter, L, Poliakov, A, Rubin, EM and Dubchak, I (2004) VISTA: computational tools for comparative genomics. Nucleic Acids Research 32: W273–W279.Google Scholar
Gupta, V and Gudu, S (1991) Interspecific hybrids and possible phylogenetic relations in grain amaranths. Euphytica 52: 33–38.Google Scholar
Hong, S-Y, Cheon, K-S, Yoo, K-O, Lee, H-O, Cho, K-S, Sih, J-T, Kim, S-J, Nam, J-H, Sohm, J-B and Kim, Y-H (2017) Complete chloroplast genome sequences and comparative analysis of Chenopodium quinoa and C. album. Frontiers in Plant Science 8: 1696.Google Scholar
Huang, Y-Y, Matzke, AJM and Matzke, M (2013) Complete sequence and comparative analysis of the chloroplast genome of coconut palm (Cocos nucifera). PLoS ONE 8: e74736.Google Scholar
Huelsenbeck, JP and Ronquist, F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics (Oxford, England) 17: 754–755.Google Scholar
Jansen, RK and Ruhlman, TA (2012) Plastid genomes of seed plants. In: Genomics of Chloroplasts and Mitochondria. Springer, pp. 103–126.Google Scholar
Katoh, K, Misawa, K, Kuma, K and Miyata, T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research 30: 3059–3066.Google Scholar
Lanta, V, Havranek, P and Ondrej, V (2003) Morphometry analysis and seed germination of Amaranthus cruentus, A. retroflexus and their hybrid (A. x turicensis). Plant Soil and Environment 49: 364–369.Google Scholar
Librado, P and Rozas, J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics (Oxford, England) 25: 1451–1452.Google Scholar
Lohse, M, Drechsel, O, Kahlau, S and Bock, R (2013) OrganellarGenomeDRAW – a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Research 41: W575–W581.Google Scholar
Ogundipe, OT and Chase, M (2009) Phylogenetic analyses of Amaranthaceae based on matK DNA sequence data with emphasis on West African species. Turkish Journal of Botany 33: 153–161.Google Scholar
Park, Y-H (2015) A taxonomic study of genus Amaranthus in Korea. Master Thesis, Graduate school of Kangwon National University.Google Scholar
Qian, J et al. (2013) The complete chloroplast genome sequence of the medicinal plant Salvia miltiorrhiza. PLoS ONE 8: e57607.Google Scholar
Sauer, JD (1967) The grain amaranths and their relatives: a revised taxonomic and geographic survey. Annals of the Missouri Botanical Garden 54: 103–137.Google Scholar
Stamatakis, A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics (Oxford, England) 22: 2688–2690.Google Scholar
Stetter, MG and Schmid, KJ (2017) Analysis of phylogenetic relationships and genome size evolution of the Amaranthus genus using GBS indicates the ancestors of an ancient crop. Molecular Phylogenetics and Evolution 109: 80–92.Google Scholar
The Angiosperm Phylogeny G (2009) An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants. APG III Botanical Journal of the Linnean Society 161: 105–121.Google Scholar
Venskutonis, PR and Kraujalis, P (2013) Nutritional components of amaranth seeds and vegetables: a review on composition, properties, and uses. Comprehensive Reviews in Food Science and Food Safety 12: 381–412.Google Scholar
Viljoen, E, Odeny, DA, Coetzee, MPA, Berger, DK and Rees, DJG (2018) Application of chloroplast phylogenomics to resolve species relationships within the plant genus Amaranthus. Journal of Molecular Evolution 86: 216–239.Google Scholar
Wang, W, Yu, H, Wang, J, Lei, W, Gao, J, Qiu, X and Wang, J (2017) The complete chloroplast genome sequences of the medicinal plant Forsythia suspensa (Oleaceae). International Journal of Molecular Sciences 18: 2288.Google Scholar
Waselkov, JE, Boleda, AS and Olsen, KM (2018) A phylogeny of the genus Amaranthus (amaranthaceae) based on several low-copy nuclear loci and chloroplast regions. Systematic Botany 43: 439–458.Google Scholar
Wyman, SK, Jansen, RK and Boore, JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics (Oxford, England) 20: 3252–3255.Google Scholar
Xu, F and Sun, M (2001) Comparative analysis of phylogenetic relationships of grain amaranths and their wild relatives (Amaranthus; Amaranthaceae) using internal transcribed spacer, amplified fragment length polymorphism, and double-primer fluorescent intersimple sequence repeat markers. Molecular Phylogenetics and Evolution 21: 372–387.Google Scholar
Yang, Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution 24: 1586–1591.Google Scholar
Supplementary material: File

Hong et al. supplementary material

Hong et al. supplementary material 1

Download Hong et al. supplementary material(File)
File 4.6 MB