Abstract
Simple SummaryAristidoideae is a subfamily of 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 and eight non-coding sequences. All Maximum Likelihood and Bayesian Inference trees strongly support the monophyly of Aristidoideae and each of the three genera. Within Aristidoideae, Aristida is 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.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.
Highlights
The subfamily Aristidoideae, together with Panicoideae, Chloridoideae, Micrairoideae, Arundinoideae, and Danthonioideae, forms the PACMAD clade of Poaceae [1]
Comparison of all 16 Aristidoideae plastomes found that they were highly conserved in genome size, gene number, structure, and inverted repeat (IR) boundary
A total of 12 highly variable regions were identified, which could be used as potential markers for phylogenetics, population genetics, and biogeography of Aristidoideae
Summary
The subfamily Aristidoideae, together with Panicoideae, Chloridoideae, Micrairoideae, Arundinoideae, and Danthonioideae, forms the PACMAD clade of Poaceae [1]. The inflorescence type of Aristidoideae has spread or contracted panicles, with only one fertile floret in one spikelet. Their leaves are narrow and usually rolled longitudinally, which is related to their adaptation to arid environments [2,3]. Aristida, Stipagrostis, and Sartidia, are contained in Aristidoideae. The core genus is Aristida, with about 300 species, which are widely distributed in temperate and subtropical arid areas [4]. Six species are contained in Sartidia, and they often occur in grasslands and savannas [3,6]. Aristidoideae has twice-independent C4 origins, once in Aristida and the other in Stipagrostis. Aristida (except for A. longifolia, which is the earliest diverging taxa in Aristida and it’s a C3 plant) and Stipagrostis are C4 photosynthesis species, while Sartidia species are C3 plants [5]
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