Phylogenetic studies and comparative chloroplast genome analyses elucidate the basal position of halophyte Nitraria sibirica (Nitrariaceae) in the Sapindales

Lu Lu, Xia Li, Zhaodong Hao, Liming Yang, Jingbo Zhang, Ye Peng, Haibin Xu, Ye Lu, Jin Zhang, Jisen Shi, Jinhui Chen, Tielong Cheng

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Nitraria sibirica is a halophyte and belongs to the family Nitrariaceae. The chloroplast genome of Nitraria sibirica (159,466 bp) has a quadripartite structure, which consists of a large single-copy (87,914 bp) region, a small single-copy (18,316 bp) region, and a pair of inverted repeats (26,618 bp). Sequencing analyses indicate that the chloroplast genome contains 113 distinct genes, including 79 peptide-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. We also identified 105 perfect simple sequence repeats, 12 most divergent non-coding regions, and 6 most divergent coding regions when compared to the chloroplast genomes of the Sapindales plants. Phylogenetic analyses using the concatenated amino acid sequences of 58 protein-coding genes from 48 species suggest that the ‘basal’ position of Nitraria sibirica belongs to the Sapindales clade. We also found that the inverted repeat expansion resulted in a duplication of rps19 in Nitraria sibirica when comparing its chloroplast genome structure with Theobroma cacao, Vitis vinifera, Eucalyptus erythrocorys and Arabidopsis thaliana. The duplication of rps19 gene was consistent with that in Zanthoxylum piperitum, Azadirachta indica, Sapindus mukorossi and Citrus sinensis, all of which belong to the order Sapindales, but different from most Rosids plants. In summary, the analyses of Nitraria sibirica chloroplast genome not only provide insights into comparative genome analysis, but also pave the way for a better understanding of the phylogenetic relationships within the Sapindales.

Original languageEnglish (US)
Pages (from-to)1-11
Number of pages11
JournalMitochondrial DNA Part A: DNA Mapping, Sequencing, and Analysis
DOIs
StateAccepted/In press - Jul 13 2017

Fingerprint

Chloroplast Genome
Sapindus
Zanthoxylum
Azadirachta
Genes
Eucalyptus
Gene Duplication
Cacao
Vitis
Transfer RNA
rRNA Genes
Arabidopsis
Microsatellite Repeats
Amino Acid Sequence
Genome
Peptides
Proteins

Keywords

  • comparative chloroplast genome
  • inverted repeat expansion
  • Nitraria sibirica
  • phylogenetic analysis

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Phylogenetic studies and comparative chloroplast genome analyses elucidate the basal position of halophyte Nitraria sibirica (Nitrariaceae) in the Sapindales. / Lu, Lu; Li, Xia; Hao, Zhaodong; Yang, Liming; Zhang, Jingbo; Peng, Ye; Xu, Haibin; Lu, Ye; Zhang, Jin; Shi, Jisen; Chen, Jinhui; Cheng, Tielong.

In: Mitochondrial DNA Part A: DNA Mapping, Sequencing, and Analysis, 13.07.2017, p. 1-11.

Research output: Contribution to journalArticle

Lu, Lu ; Li, Xia ; Hao, Zhaodong ; Yang, Liming ; Zhang, Jingbo ; Peng, Ye ; Xu, Haibin ; Lu, Ye ; Zhang, Jin ; Shi, Jisen ; Chen, Jinhui ; Cheng, Tielong. / Phylogenetic studies and comparative chloroplast genome analyses elucidate the basal position of halophyte Nitraria sibirica (Nitrariaceae) in the Sapindales. In: Mitochondrial DNA Part A: DNA Mapping, Sequencing, and Analysis. 2017 ; pp. 1-11.
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AU - Li, Xia

AU - Hao, Zhaodong

AU - Yang, Liming

AU - Zhang, Jingbo

AU - Peng, Ye

AU - Xu, Haibin

AU - Lu, Ye

AU - Zhang, Jin

AU - Shi, Jisen

AU - Chen, Jinhui

AU - Cheng, Tielong

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AB - Nitraria sibirica is a halophyte and belongs to the family Nitrariaceae. The chloroplast genome of Nitraria sibirica (159,466 bp) has a quadripartite structure, which consists of a large single-copy (87,914 bp) region, a small single-copy (18,316 bp) region, and a pair of inverted repeats (26,618 bp). Sequencing analyses indicate that the chloroplast genome contains 113 distinct genes, including 79 peptide-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. We also identified 105 perfect simple sequence repeats, 12 most divergent non-coding regions, and 6 most divergent coding regions when compared to the chloroplast genomes of the Sapindales plants. Phylogenetic analyses using the concatenated amino acid sequences of 58 protein-coding genes from 48 species suggest that the ‘basal’ position of Nitraria sibirica belongs to the Sapindales clade. We also found that the inverted repeat expansion resulted in a duplication of rps19 in Nitraria sibirica when comparing its chloroplast genome structure with Theobroma cacao, Vitis vinifera, Eucalyptus erythrocorys and Arabidopsis thaliana. The duplication of rps19 gene was consistent with that in Zanthoxylum piperitum, Azadirachta indica, Sapindus mukorossi and Citrus sinensis, all of which belong to the order Sapindales, but different from most Rosids plants. In summary, the analyses of Nitraria sibirica chloroplast genome not only provide insights into comparative genome analysis, but also pave the way for a better understanding of the phylogenetic relationships within the Sapindales.

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