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The complete chloroplast genome sequence of Pseudoroegneria libanotica, genomic features, and phylogenetic relationship with Triticeae species

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Biologia Plantarum

Abstract

Pseudoroegneria libanotica is an important herbage diploid species possessing the St genome. The St genome participates in the formation of nine perennial genera in Triticeae (Poaceae). The whole chloroplast (cp) genome of P. libanotica is 135 026 bp in length. The typical quadripartite structure consists of one large single copy of 80 634 bp, one small single copy of 12 766 bp and a pair of inverted regions (20 813 bp each). The cp genome contains 76 coding genes, four ribosomal RNA and 30 transfer RNA genes. Comparative sequence analysis suggested that: 1) the 737 bp deletion in the cp of P. libanotica was specific in Triticeae species and might transfer into its nuclear genome; 2) hot-spot regions, indels in intergenic regions and protein coding sequences mainly led to the length variation in Triticeae; 3) highly divergence regions combined with negative selection in rpl2, rps12, ccsA, rps8, ndhH, petD, ndhK, psbM, rps3, rps18, and ndhA were identified as effective molecular markers and could be considered in future phylogenetic studies of Triticeae species; and 4) ycf3 gene with rich cpSSRs was suitable for phylogeny analysis or could be used for DNA barcoding at low taxonomic levels. The cpSSRs distribution in the coding regions of diploid Triticeae species was shown for the first time and provided a valuable source for developing primers to study specific simple sequence repeat loci.

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Abbreviations

BS:

bootstrap value

CNS:

conserved noncoding sequences

cp:

chloroplast

cpSSR:

chloroplast simple sequence repeat

dN/dS :

ratio of nonsynonymous and synonymous substitution rates

indel:

insertion and deletion

IR:

inverted region

LSC:

large single copy

ML:

maximum likelihood

rRNA:

ribosomal RNA

SSC:

small single copy

TE:

transposable element

tRNA:

transfer RNA

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Authors and Affiliations

  1. Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, P. R. China

    D. D. Wu, L. N. Sha, C. Tang, X. Fan, Y. Wang, H. Y. Kang, H. Q. Zhang & Y. H. Zhou

  2. Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, P. R. China

    D. D. Wu & Y. H. Zhou

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  1. D. D. Wu
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  2. L. N. Sha
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  3. C. Tang
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  4. X. Fan
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  5. Y. Wang
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  7. H. Q. Zhang
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  8. Y. H. Zhou
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Correspondence to Y. H. Zhou.

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Acknowledgments: The authors are thankful to the National Natural Science Foundation of China (Grant Nos. 31470305, 31270243, and 31200252), the National Key Research and Development of China (2016YFD0102000), and the fund from the Science and Technology Bureau and Education Bureau of Sichuan Province, China. We are very grateful to the American National Plant Germplasm System (Pullman, Washington, USA) for providing seed material for this study. The first two authors contributed equally to this work.

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Wu, D.D., Sha, L.N., Tang, C. et al. The complete chloroplast genome sequence of Pseudoroegneria libanotica, genomic features, and phylogenetic relationship with Triticeae species. Biol Plant 62, 231–240 (2018). https://doi.org/10.1007/s10535-017-0759-y

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