Complete Chloroplast Genome of an Endangered Species Quercus litseoides, and Its Comparative, Evolutionary, and Phylogenetic Study with Other Quercus Section Cyclobalanopsis Species

Li, Yu; Wang, Tianrui; Kozlowski, Gregor; Li, Meihua; Yi, Long

doi:10.3390/genes13071184

Cited by 14 publications

(27 citation statements)

References 73 publications

(93 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The SSRs are used to be the molecular markers, in particular, in studies of biogeography and plant population genetics and the identification of species because they have high polymorphic rates [ 45 ]. Therefore, those fragments, such as (AAAT)3 only found in the intergenic region ( trn S / psbZ ) in F. kirialovii and (A)15 observed in the ndhF gene only in T. transiliensis , may be useful for selecting as molecular markers to differentiate between Ferula species in the future.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2023

View full text Add to dashboard Cite

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.

show abstract

Section: Discussionmentioning

confidence: 99%

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

et al. 2023

View full text Add to dashboard Cite

show abstract

“…2022 ), Castanopsis fargesii NC_047230.1 (Li et al. 2022 ), Castanopsis carlesii NC_057119.1 (Wang et al. 2022 ), Castanopsis sclerophylla MT627605.1 (Miao et al.…”

Section: Resultsmentioning

confidence: 99%

The complete chloroplast genome sequence of Castanopsis fordii Hance (Fagaceae)

Wang

Huang

et al. 2023

Mitochondrial DNA Part B

View full text Add to dashboard Cite

Castanopsis fordii Hance 1884 is a typical evergreen broad-leaved forest plant in the south subtropical and middle subtropical regions of China. It has high utilization value in wood production and soil erosion protection. Here, we first reported and characterized the complete chloroplast (cp) genome sequence of C. fordii based on Illumina paired-end sequencing data. The complete cp genome sequence of C. fordii was 160,853 base pairs (bp) in length which contained two inverted repeats (IRs) of 25,699 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 90,474 bp and 18,981 bp, respectively. The cpDNA contained 129 genes, comprising 85 protein-coding genes, 36 tRNA genes, 8 rRNA genes. The overall GC content of the plastome was 36.8%. Phylogenetic analysis base on 14 chloroplast genomes indicated that C. fordii was closely related to the species C. tibetana and C. concinna in Fagaceae.

show abstract

“…Vahl, Olea europaea Hoffmanns. & Link L., and Quercus litseoides Dunn [ 67 , 68 ], and were fully encoded by the IR regions in Polystachya adansoniae Rchb.f., Polystachya bennettiana Rchb.f., and Dracaena cinnabari Balf.f. [ 69 , 70 ].…”

Section: Discussionmentioning

confidence: 99%

Ten Plastomes of Crassula (Crassulaceae) and Phylogenetic Implications

Ding

Han

et al. 2022

Biology

View full text Add to dashboard Cite

The genus Crassula is the second-largest genus in the family Crassulaceae, with about 200 species. As an acknowledged super-barcode, plastomes have been extensively utilized for plant evolutionary studies. Here, we first report 10 new plastomes of Crassula. We further focused on the structural characterizations, codon usage, aversion patterns, and evolutionary rates of plastomes. The IR junction patterns—IRb had 110 bp expansion to rps19—were conservative among Crassula species. Interestingly, we found the codon usage patterns of matK gene in Crassula species are unique among Crassulaceae species with elevated ENC values. Furthermore, subgenus Crassula species have specific GC-biases in the matK gene. In addition, the codon aversion motifs from matK, pafI, and rpl22 contained phylogenetic implications within Crassula. The evolutionary rates analyses indicated all plastid genes of Crassulaceae were under the purifying selection. Among plastid genes, ycf1 and ycf2 were the most rapidly evolving genes, whereas psaC was the most conserved gene. Additionally, our phylogenetic analyses strongly supported that Crassula is sister to all other Crassulaceae species. Our findings will be useful for further evolutionary studies within the Crassula and Crassulaceae.

show abstract

Complete Chloroplast Genome of an Endangered Species Quercus litseoides, and Its Comparative, Evolutionary, and Phylogenetic Study with Other Quercus Section Cyclobalanopsis Species

Cited by 14 publications

References 73 publications

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

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

The complete chloroplast genome sequence of Castanopsis fordii Hance (Fagaceae)

Ten Plastomes of Crassula (Crassulaceae) and Phylogenetic Implications

Contact Info

Product

Resources

About