Complete chloroplast genomes of Achnatherum inebrians and comparative analyses with related species from Poaceae

Abstract

This paper reports the complete chloroplast genome of Achnatherum inebrians, a poisonous herb that is widely distributed in the rangelands of Northern China. The genome is 137,714 bp in total, and consists of a large single-copy (LSC, 81,758 bp) and small single-copy (SSC, 12,682 bp) region separated by a pair of inverted repeats (IRs, 21,637 bp). The genome contains 130 genes, including 84 protein-coding genes, 38 tRNA genes and 8 ribosomal RNA genes, and the GC content is 36.17%. We subsequently performed comparative analysis of complete genomes from A.inebrians and other Poaceae related species from GenBank. Thirty-eight simple sequence repeats (SSRs) were identified, further demonstrating rapid evolution in Poaceae. Finally, the phylogenetic trees of 37 species of Poaceae and two species of Amaranthaceae were constructed by using Maximum likelihood (ML) and Bayesian Inference (BI) methods, based on the genes of the complete chloroplast genome. We identified hotspots which can be used as molecular markers and barcodes for phylogenetic analysis as well as for species identification. Phylogenetic analysis indicated that A. inebrians is a member of the genus Stipa rather than Achnatherum.

Phylogenetic significance of the characteristics of simple sequence repeats at the genus level based on the complete chloroplast genome sequences of Cyatheaceae

“…Mononucleotide SSRs which exist in a large numbers in cp genomes (George et al., 2015 ; Liang et al., 2019 ) are the most abundant (Table 3 ), and A/T motifs are the most common (Figure 3 ; Appendix Table S9 ). This finding is similar to previously reported patterns of land plants (George et al., 2015 ; Huang et al., 2021 ; Ren et al., 2021 ; Vieira et al., 2014 ; Wei et al., 2021 ). However, in Polypodiaceae plastomes, most repeats were C/G mononucleotides.…”

“…SSRs were detected in the CDS region of Alsophila and Sphaeropteris , and SSRs were detected only in the rRNA gene of Sphaeropteris (Appendix Table S10 ). The cpSSRs of each species were mainly distributed in the IGS region and LSC regions, which is consistent with that reported in Adrinandra (Nguyen et al., 2021 ), Blumea (Abdullah et al., 2021 ), Mikania (Su et al., 2018 ), Prunus (Huang et al., 2021 ), Cupressaceae (Ping et al., 2021 ), Poaceae (Wei et al., 2021 ), Polypodiaceae (Liu et al., 2021 ), and ferns (Fan et al., 2021 ). Alsophila had the highest relative abundance and density (0.77–0.78/kb, 9.81–9.82 bp/kb, respectively) of the SSRs in the cp genome, and the lowest relative abundance and density (0.40/kb, 4.11–5.06 bp/kb) were found in Gymnosphaera .…”

“…Recent studies have shown minimal differences in the distribution patterns and numbers of SSRs among cpSSRs of the related species (Fan et al., 2021 ; Liu et al., 2021 ; Ping et al., 2021 ; Wei et al., 2021 ). Comparative analysis of cpSSRs from broad plant groups may be useful for a better understanding of the diversity and evolutionary trends of cp genomes (George et al., 2015 ).…”

“…Mikania (Su et al, 2018), Prunus (Huang et al, 2021), Cupressaceae (Ping et al, 2021), Poaceae (Wei et al, 2021), Polypodiaceae (Liu et al, 2021), and ferns (Fan et al, 2021). Alsophila had the highest relative abundance and density (0.77-0.78/kb, 9.81-9.82 bp/kb, respectively) of the SSRs in the cp genome, and the lowest relative abundance and density (0.40/kb, 4.11-5.06 bp/kb) were found in Gymnosphaera.…”

“…In the recent studies, eight Cyatheaceae species were divided into three genera (Ching, 1978;Dong & Zuo, 2018;Janssen & Rakotondrainibe, 2008;Korall et al, 2007;Korall & Pryer, 2014;Smith et al, 2006) or two genera (PPG I, 2016;Xia, 1989;Zhang & Nishida, 2013) Recent studies have shown minimal differences in the distribution patterns and numbers of SSRs among cpSSRs of the related species (Fan et al, 2021;Liu et al, 2021;Ping et al, 2021;Wei et al, 2021).…”