Comparative and Phylogenetic Analysis of Complete Plastomes among Aristidoideae Species (Poaceae)

Abstract

Aristidoideae is a subfamily in the PACMAD clade of family Poaceae, including three genera, Aristida, Stipagrostis, and Sartidia. In this study, the plastomes of Aristida adscensionis and Stipagrostis pennata were newly sequenced, and a total of 16 Aristidoideae plastomes were compared. All plastomes were conservative in genome size, gene number, structure, and IR boundary. Repeat sequence analysis showed that forward and palindrome repeats were the most common repeat types. The number of SSRs ranged from 30 (Sartidia isaloensis) to 54 (Aristida purpurea). Codon usage analysis showed that plastome genes preferred to use codons ending with A/T. A total of 12 highly variable regions were screened, including four protein coding sequences (matK, ndhF, infA, and rpl32) and eight non-coding sequences (rpl16-1-rpl16-2, ccsA-ndhD, trnY-GUA-trnD-GUC, ndhF-rpl32, petN-trnC-GCA, trnT-GGU-trnE-UUC, trnG-GCC-trnfM-CAU, and rpl32-trnL-UAG). Furthermore, the phylogenetic position of this subfamily and their intergeneric relationships need to be illuminated. All Maximum Likelihood and Bayesian Inference trees strongly support the monophyly of Aristidoideae and each of three genera, and the clade of Aristidoideae and Panicoideae was a sister to other subfamilies in the PACMAD clade. Within Aristidoideae, Aristida is a sister to the clade composed of Stipagrostis and Sartidia. The divergence between C4 Stipagrostis and C3 Sartidia was estimated at 11.04 Ma, which may be associated with the drought event in the Miocene period. Finally, the differences in carbon fixation patterns, geographical distributions, and ploidy may be related to the difference of species numbers among these three genera. This study provides insights into the phylogeny and evolution of the subfamily Aristidoideae.

Chloroplast genomes of four Carex species: Long repetitive sequences trigger dramatic changes in chloroplast genome structure

“…Arginine (Arg), proline (Pro), and threonine (Thr) also had a strong preference for using codons with maximum RSCU values greater than 1.80. In addition, RSCU values of four Carex species showed significantly lower nucleotide abundance of G or C than of A or T at the third codon position (14.7 < 45.3); this is similar to other studies of chloroplast genomes (Poczai and Hyvonen, 2017;Ren et al, 2021;Guo et al, 2022).…”

“…It is now widely accepted that the use of synonymous codons is not random and that analysis of codon preferences can provide valuable information for understanding species adaptation and molecular evolution (Plotkin and Kudla, 2011;Leffler et al, 2012). The chloroplast genomes of four Carex species contain 30 highfrequency codons (RSCU > 1) and prefers codons ending in A/T, similar to other closely related taxa (Poczai and Hyvonen, 2017;Chakraborty et al, 2020;Ren et al, 2021;Guo et al, 2022). Variation in codon bias among Carex species was not significant, with only minor differences in optimal codons for valine (Val) (GUA in C. littledalei, with GUU in C. breviculmis, C. lithophila, C. siderosticta).…”

Comparison of chloroplast genomes and phylogenomics in the Ficus sarmentosa complex (Moraceae)

“…Although chloroplast genomes exhibit high conservation among closely related species, discrepancy and heterogeneity have also been widely observed across the whole genomes. Overall, the variable sites of the two single-copy regions (LSC and SSC) are more abundant than IR regions in both the genus Ficus (Fig 5) and most other plant groups [56,70,71]. Chloroplast regions with different mutation rates are appropriate for a range of evolutionary research.…”

Structural Characterization of the Acer ukurunduense Chloroplast Genome Relative to Related Species in the Acer Genus

“…The trnK-UUU/rps16 has been successfully used to confirm the evolutionary relationship and complete Latin name changes of the Sium alliance within the Apiaceae tribe Oenantheae ( Spalik et al, 2009 ). The phylogenetic analysis based on sequencing data from different molecular markers ndhF/rpl32 and rpl32/trnL-UAG is also separate in the families Aristidoideae and Eragrostideae, and in the genuses Fagopyrum and Dolomiaea , respectively ( Shen et al, 2020 ; Fan et al, 2021 ; Kuan Liu et al, 2021 ; Guo et al, 2022 ). The ycf1 has been employed to assist in inferring the evolution of Pinus , Hoya , and Curcuma ( Liang et al, 2020 ; Odago et al, 2021 ; Zeb et al, 2022 ).…”