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

• Published in: Biology (Basel, Switzerland) Vol. 11; no. 1; p. 63
• Main Authors: Guo, Xiu-Xiu, Qu, Xiao-Jian, Zhang, Xue-Jie, Fan, Shou-Jin
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 02.01.2022; MDPI
• Subjects: Aristida; Aristida adscensionis; Aristida purpurea; Aristidoideae; Bayesian analysis; Carbon fixation; Chloroplasts; Codons; comparative genomics; Divergence; Drought; Genes; Genomes; Geographical distribution; Miocene; Nucleotide sequence; Phylogenetics; phylogenomics; Phylogeny; plastome; Plastomes; Ploidy; Poaceae; Sequence analysis; Species; species diversification; Trees; Working groups; Beijing China; United States > US; China; species diversification; Aristidoideae; plastome; comparative genomics; phylogenomics
• ISSN: 2079-7737; 2079-7737
• DOI: 10.3390/biology11010063

Aristidoideae is a subfamily in the PACMAD clade of family Poaceae, including three genera, , , and In this study, the plastomes of and 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 ( ) to 54 ( ). 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 ( K, F, A, and 32) and eight non-coding sequences ( 16-1- 16-2, A- D, Y-GUA- D-GUC, F- 32, N- C-GCA, T-GGU- E-UUC, G-GCC- fM-CAU, and 32- L-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, is a sister to the clade composed of and . The divergence between C and C 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.