Analysis of Chloroplast Genomes Provides Insights Into the Evolution of Agropyron

Han, Huijie; Qiu, Rui; Ye-fei, Liu; Zhou, Xinyue; Gao, Cuiping; Pang, Yongzhen; Zhao, Yan

doi:10.3389/fgene.2022.832809

Cited by 16 publications

(14 citation statements)

References 35 publications

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“…All Leymus species showed minor variations in junction positions of JLB (~13 bp), JSB (~34 bp), and JLA (~8 bp) ( Figure 7 ). In addition, ndhH was found to straddle the JSA, which is consistent with previous data on other Triticeae species, such as Agropyron , Hordeum , and Festuca [ 23 , 47 , 58 , 59 ]. The different position of ndhH in the JSA border suggests that these variations may be caused by intramolecular recombination during early evolution [ 60 , 61 , 62 ].…”

Section: Discussionsupporting

confidence: 91%

“…It is observed that the number of SSRs in the non-coding region was higher than that in the coding region ( Table S5 ). These results are similar to those of other Triticeae species [ 23 , 47 , 48 ] and may be the reason why the mutation rate in IGS regions is higher than in the coding regions [ 49 ].…”

Section: Discussionsupporting

confidence: 87%

“…The IR regions of the cp genome are considered to be the most conserved regions [ 55 ]. Similar to previous studies on Triticeae, all 16 Leymus species had the same gene arrangement, in which six protein-coding genes ( rpl2 , rpl23 , rps12 , ndhB , rps15, and rps19 ) were duplicated [ 23 , 43 , 47 ]. Moreover, we identified the smallest reverse IR region in L. angustus (20,813 bp) and the largest in L. komarovii (21,578 bp) ( Table S3 ).…”

Section: Discussionsupporting

confidence: 69%

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Comparative and Phylogenetic Analysis of Complete Chloroplast Genomes in Leymus (Triticodae, Poaceae)

Tian

Yang

et al. 2022

Genes

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Leymus is a perennial genus that belongs to the tribe Triticeae (Poaceae) which has an adaptive capacity to ecological conditions and strong resistance to cold, drought, and salinity. Most Leymus species are fine herbs that can be used for agriculture, conservation, and landscaping. Due to confusion taxonomy within genera, the complete chloroplast (cp) genome of 13 Leymus species was sequenced, assembled, and compared with those of three other previously published Leymus species (Leymus condensatus, Leymus angustus, and Leymus mollis) to clarify the issue. Overall, the whole cp genome size ranged between 135,057 (L. condensatus) and 136,906 bp (Leymus coreanus) and showed a typical quadripartite structure. All studied species had 129 genes, including 83 protein-coding genes, 38 transfer RNAs, and 8 ribosomal RNAs. In total, 800 tandem repeats and 707 SSR loci were detected, most of which were distributed in the large single-copy region, followed by the inverted repeat (IR) and small single-copy regions. The sequence identity of all sequences was highly similar, especially concerning the protein-coding and IR regions; in particular, the protein-coding regions were significantly similar to those in the IR regions, regardless of small sequence differences in the whole cp genome. Moreover, the coding regions were more conserved than the non-coding regions. Comparisons of the IR boundaries showed that IR contraction and expansion events were reflected in different locations of rpl22, rps19, ndhH, and psbA genes. The close phylogenetic relationship of Leymus and Psathyrostachys indicated that Psathyrostachys possibly is the donor of the Ns genome sequence identified in Leymus. Altogether, the complete cp genome sequence of Leymus will lay a solid foundation for future population genetics and phylogeography studies, as well as for the analysis of the evolution of economically valuable plants.

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Section: Discussionsupporting

confidence: 91%

Section: Discussionsupporting

confidence: 87%

Section: Discussionsupporting

confidence: 69%

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Comparative and Phylogenetic Analysis of Complete Chloroplast Genomes in Leymus (Triticodae, Poaceae)

Tian

Yang

et al. 2022

Genes

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“…The obvious nucleotide bias may be due to the lower number of hydrogen bonds and lower energy consumption of A/T bases (Niu et al, 2017;Kim and Cheon, 2021). Previous studies have reported a higher A/T than G/C content in most plants, which may be due to the large number of A/T-type SSRs (Wang et al, 2021;Wu et al, 2021;Han et al, 2022). In this study, we analyzed the number, location, and composition of SSRs in the cp genomes of five Artemisia species and provided a new reference for further research on molecular markers, mutation hotspots, population genetics, and crop breeding.…”

Section: Figurementioning

confidence: 99%

Comparative and phylogenetic analysis of complete chloroplast genomes from five Artemisia species

et al. 2022

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Artemisia Linn. is a large genus within the family Asteraceae that includes several important medicinal plants. Because of their similar morphology and chemical composition, traditional identification methods often fail to distinguish them. Therefore, developing an effective identification method for Artemisia species is an urgent requirement. In this study, we analyzed 15 chloroplast (cp) genomes, including 12 newly sequenced genomes, from 5 Artemisia species. The cp genomes from the five Artemisia species had a typical quadripartite structure and were highly conserved across species. They had varying lengths of 151,132–151,178 bp, and their gene content and codon preferences were similar. Mutation hotspot analysis identified four highly variable regions, which can potentially be used as molecular markers to identify Artemisia species. Phylogenetic analysis showed that the five Artemisia species investigated in this study were sister branches to each other, and individuals of each species formed a monophyletic clade. This study shows that the cp genome can provide distinguishing features to help identify closely related Artemisia species and has the potential to serve as a universal super barcode for plant identification.

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“…Therefore, the plastome is a useful tool to improve the certainty of phylogenetic trees [ 27 , 28 ]. The plastome generally is 115 to 165 kb in length, containing a large single-copy region (LSC), two separately inverted repeat regions (IRs), and one small single-copy region (SSC), and encodes about 110–130 unique genes [ 29 – 31 ]. Comparative analysis of plastomes reveals the variation in its structural combination and gene arrangement, which is helpful to further identify the mutational hotspots for species authentication [ 32 , 33 ].…”

Section: Introductionmentioning

confidence: 99%

The plastid genome of twenty-two species from Ferula, Talassia, and Soranthus: comparative analysis, phylogenetic implications, and adaptive evolution

et al. 2023

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Background The Ferula genus encompasses 180–185 species and is one of the largest genera in Apiaceae, with many of Ferula species possessing important medical value. The previous studies provided more information for Ferula, but its infrageneric relationships are still confusing. In addition, its genetic basis of its adaptive evolution remains poorly understood. Plastid genomes with more variable sites have the potential to reconstruct robust phylogeny in plants and investigate the adaptive evolution of plants. Although chloroplast genomes have been reported within the Ferula genus, few studies have been conducted using chloroplast genomes, especially for endemic species in China. Results Comprehensively comparative analyses of 22 newly sequenced and assembled plastomes indicated that these plastomes had highly conserved genome structure, gene number, codon usage, and repeats type and distribution, but varied in plastomes size, GC content, and the SC/IR boundaries. Thirteen mutation hotspot regions were detected and they would serve as the promising DNA barcodes candidates for species identification in Ferula and related genera. Phylogenomic analyses with high supports and resolutions showed that Talassia transiliensis and Soranthus meyeri were nested in the Ferula genus, and thus they should be transferred into the Ferula genus. Our phylogenies also indicated the monophyly of subgenera Sinoferula and subgenera Narthex in Ferula genus. Twelve genes with significant posterior probabilities for codon sites were identified in the positively selective analysis, and their function may relate to the photosystem II, ATP subunit, and NADH dehydrogenase. Most of them might play an important role to help Ferula species adapt to high-temperatures, strong-light, and drought habitats. Conclusion Plastome data is powerful and efficient to improve the support and resolution of the complicated Ferula phylogeny. Twelve genes with significant posterior probabilities for codon sites were helpful for Ferula to adapt to the harsh environment. Overall, our study supplies a new perspective for comprehending the phylogeny and evolution of Ferula.

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Analysis of Chloroplast Genomes Provides Insights Into the Evolution of Agropyron

Cited by 16 publications

References 35 publications

Comparative and Phylogenetic Analysis of Complete Chloroplast Genomes in Leymus (Triticodae, Poaceae)

Comparative and Phylogenetic Analysis of Complete Chloroplast Genomes in Leymus (Triticodae, Poaceae)

Comparative and phylogenetic analysis of complete chloroplast genomes from five Artemisia species

The plastid genome of twenty-two species from Ferula, Talassia, and Soranthus: comparative analysis, phylogenetic implications, and adaptive evolution

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