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

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) hotspot 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.

Variation in Plastome Sizes Accompanied by Evolutionary History in Monogenomic Triticeae (Poaceae: Triticeae)

“…The disappearance of ycf 2 might indicate that this function region has been transferred to a nuclear genome. Wu et al (2017) found that this deletion was exactly similar (identities = 99%) to a genomic scaffold of chromosome 3B of T. aestivum , and that it possesses high similarity (identify = 98%) with cp sequences in Pooideae species, but the specific function is still unknown. Although many species in different lineages contain an intact ycf 15 gene (encoding the beta subunit of acetyl-CoA carboxylase complex) and have been annotated in several sequenced chloroplast genomes, e.g., several Asterids , Magnolia ( Kuang et al, 2011 ), and Piper ( Cai et al, 2006 ), it is almost impossible to determine whether this gene is able to encode a functional protein or how it has evolved in angiosperms so far.…”

“…A ∼800-bp length variation in IR was detected between trn I and trn L, which mainly contained pseudogenes ycf 2 and ycf 15. Wu et al (2017) suggested that this deletion in the cp of P. libanotica was specific in Triticeae species. We confirmed that the loss of pseudogenes ycf 2 and ycf 15 occurred in the cp of Pseudoroegneria , Dasypyrum , Lophopyrum , and Thinopyrum .…”

“…The retained pseudogenes and replicates might participate in some nucleo-plasmic interactions to promote gene function. Although the acc D, ycf 2, and ycf 15 genes had been lost from the plastid genome several times in angiosperms, their functions were fulfilled by nuclear copies ( Nakkaew et al, 2008 ; Huang et al, 2017 ; Wu et al, 2017 ).…”

“…spontaneum , Secale cereale , were downloaded from the NCBI published data (Saski et al, 2006; Gogniashvili et al, 2014, NCBI web, Bortiri et al, 2008 ; Gornicki et al, 2014 ; Middleton et al, 2014 ; Saarela et al, 2015 ). The remaining sequences were from our previous publications ( Chen et al, 2017 , 2020 ; Wu et al, 2017 ).…”

“…Since the tribe was originated, lineage diversification of monogenomic genus in a range of evolutionary time raised the question of how cp genomes have evolved. Comparison of cp genomic structure on several monogenomic Triticeae showed that a 737-bp deletion in Pseudoroegneria libanotica might be related to potential nuclear–cytoplasm transfer ( Wu et al, 2017 ). Analysis of the cp genome sequence in Agropyron cristatum suggested that deletion of acc D and translocation of rpl 23 genes might represent an independent gene-loss event or an additional divergence in Triticeae ( Chen et al, 2017 ).…”