biologia plantarum

International journal on Plant Life established by Bohumil Němec in 1959

Biologia plantarum 62:231-240, 2018 | DOI: 10.1007/s10535-017-0759-y

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

D. D. Wu1,2, L. N. Sha1, C. Tang1, X. Fan1, Y. Wang1, H. Y. Kang1, H. Q. Zhang1, Y. H. Zhou1,2,*
1 Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, P. R. China
2 Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Wenjiang, P. R. China

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.

Keywords: hot-spot regions; phylogenetic tree; sequence transfer; simple sequence repeats
Subjects: chloroplast genome; phylogenetic tree; sequence transfer; simple sequence repeat; indels

Received: December 17, 2016; Revised: May 13, 2017; Accepted: June 6, 2017; Published: June 1, 2018  Show citation

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Wu, D.D., Sha, L.N., Tang, C., Fan, X., Wang, Y., Kang, H.Y., Zhang, H.Q., & Zhou, Y.H. (2018). The complete chloroplast genome sequence of Pseudoroegneria libanotica, genomic features, and phylogenetic relationship with Triticeae species. Biologia plantarum, 62(2), 231-240. doi: 10.1007/s10535-017-0759-y
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