The chloroplast genome of Amygdalus L. (Rosaceae) reveals the phylogenetic relationship and divergence time

Lü, Ke; Zhang, Kai; He, Yiming; Wang, Haitao; Chai, Guaiqiang; Shi, Jiannong; Duan, Yanwu

doi:10.1186/s12864-021-07968-6

Cited by 21 publications

(16 citation statements)

References 67 publications

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“…Thus, it is highly conserved in structure and gene composition. Based on these characteristics, chloroplast genome sequence data should provide robust solutions for studies on phylogenetics, molecular evolution, population genetics, and phylogeography ( Dong et al, 2013 ; Yang et al, 2020 , 2021b ; Du et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Comparative chloroplast genome analysis of Ficus (Moraceae): Insight into adaptive evolution and mutational hotspot regions

Zhang

Yang²,

Li³

et al. 2022

Front. Plant Sci.

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As the largest genus in Moraceae, Ficus is widely distributed across tropical and subtropical regions and exhibits a high degree of adaptability to different environments. At present, however, the phylogenetic relationships of this genus are not well resolved, and chloroplast evolution in Ficus remains poorly understood. Here, we sequenced, assembled, and annotated the chloroplast genomes of 10 species of Ficus, downloaded and assembled 13 additional species based on next-generation sequencing data, and compared them to 46 previously published chloroplast genomes. We found a highly conserved genomic structure across the genus, with plastid genome sizes ranging from 159,929 bp (Ficus langkokensis) to 160,657 bp (Ficus religiosa). Most chloroplasts encoded 113 unique genes, including a set of 78 protein-coding genes, 30 transfer RNA (tRNA) genes, four ribosomal RNA (rRNA) genes, and one pseudogene (infA). The number of simple sequence repeats (SSRs) ranged from 67 (Ficus sagittata) to 89 (Ficus microdictya) and generally increased linearly with plastid size. Among the plastomes, comparative analysis revealed eight intergenic spacers that were hotspot regions for divergence. Additionally, the clpP, rbcL, and ccsA genes showed evidence of positive selection. Phylogenetic analysis indicated that none of the six traditionally recognized subgenera of Ficus were monophyletic. Divergence time analysis based on the complete chloroplast genome sequences showed that Ficus species diverged rapidly during the early to middle Miocene. This research provides basic resources for further evolutionary studies of Ficus.

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Section: Introductionmentioning

confidence: 99%

Comparative chloroplast genome analysis of Ficus (Moraceae): Insight into adaptive evolution and mutational hotspot regions

Zhang

Yang²,

Li³

et al. 2022

Front. Plant Sci.

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“…The chloroplast (cp) is an organelle in plants and algae ( Du et al, 2021 ; Li et al, 2021 ) that plays a significant role in plant cell function, including in photosynthesis, carbon fixation, and stress response. The cp is a semiautonomous organelle with a relatively independent genome containing its own genetic system for replication, transcription, and translation ( Favier et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Sequence Characteristics and Phylogenetic Analysis of the Artemisia argyi Chloroplast Genome

Chen

Miao²,

Luo³

et al. 2022

Front. Plant Sci.

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Artemisia argyi Levl. et Van is an important Asteraceae species with a high medicinal value. There are abundant A. argyi germplasm resources in Asia, especially in China, but the evolutionary relationships of these varieties and the systematic localization of A. argyi in the family Asteraceae are still unclear. In this study, the chloroplast (cp) genomes of 72 A. argyi varieties were systematically analyzed. The 72 varieties originated from 47 regions in China at different longitudes, latitudes and altitudes, and included both wild and cultivated varieties. The A. argyi cp genome was found to be ∼151 kb in size and to contain 114 genes, including 82 protein-coding, 28 tRNA, and 4 rRNA genes. The number of short sequence repeats (SSRs) in A. argyi cp genomes ranged from 35 to 42, and most of them were mononucleotide A/T repeats. A total of 196 polymorphic sites were detected in the cp genomes of the 72 varieties. Phylogenetic analysis demonstrated that the genetic relationship between A. argyi varieties had a weak relationship with their geographical distribution. Furthermore, inverted repeat (IR) boundaries of 10 Artemisia species were found to be significantly different. A sequence divergence analysis of Asteraceae cp genomes showed that the variable regions were mostly located in single-copy (SC) regions and that the coding regions were more conserved than the non-coding regions. A phylogenetic tree was constructed using 43 protein-coding genes common to 67 Asteraceae species. The resulting tree was consistent with the traditional classification system; Artemisia species were clustered into one group, and A. argyi was shown to be closely related to Artemisia lactiflora and Artemisia montana. In summary, this study systematically analyzed the cp genome characteristics of A. argyi and compared cp genomes of Asteraceae species. The results provide valuable information for the definitive identification of A. argyi varieties and for the understanding of the evolutionary relationships between Asteraceae species.

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“…A comparison of 20 Indigofera plastomes revealed that rp s19, ycf 1, and ndh F demonstrated pronounced expansion or contraction, as reported in Salvia L., Amygdalus L., Iris L., Prunus L. subg. Cerasus Mill., and Asteraceae ( Du et al., 2021 ; Pascual-Diaz et al., 2021 ; Du et al., 2022 ; Feng et al., 2022a ; Li et al., 2022c ). These subtle differences in boundaries could potentially be used for species identification.…”

Section: Discussionmentioning

confidence: 99%

Phylogenomics and plastome evolution of Indigofera (Fabaceae)

et al. 2023

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IntroductionIndigofera L. is the third largest genus in Fabaceae and includes economically important species that are used for indigo dye-producing, medicinal, ornamental, and soil and water conservation. The genus is taxonomically difficult due to the high level of overlap in morphological characters of interspecies, fewer reliability states for classification, and extensive adaptive evolution. Previous characteristic-based taxonomy and nuclear ITS-based phylogenies have contributed to our understanding of Indigofera taxonomy and evolution. However, the lack of chloroplast genomic resources limits our comprehensive understanding of the phylogenetic relationships and evolutionary processes of Indigofera.MethodsHere, we newly assembled 18 chloroplast genomes of Indigofera. We performed a series of analyses of genome structure, nucleotide diversity, phylogenetic analysis, species pairwise Ka/Ks ratios, and positive selection analysis by combining with allied species in Papilionoideae.Results and discussionThe chloroplast genomes of Indigofera exhibited highly conserved structures and ranged in size from 157,918 to 160,040 bp, containing 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Thirteen highly variable regions were identified, of which trnK-rbcL, ndhF-trnL, and ycf1 were considered as candidate DNA barcodes for species identification of Indigofera. Phylogenetic analysis using maximum likelihood (ML) and Bayesian inference (BI) methods based on complete chloroplast genome and protein-coding genes (PCGs) generated a well-resolved phylogeny of Indigofera and allied species. Indigofera monophyly was strongly supported, and four monophyletic lineages (i.e., the Pantropical, East Asian, Tethyan, and Palaeotropical clades) were resolved within the genus. The species pairwise Ka/Ks ratios showed values lower than 1, and 13 genes with significant posterior probabilities for codon sites were identified in the positive selection analysis using the branch-site model, eight of which were associated with photosynthesis. Positive selection of accD suggested that Indigofera species have experienced adaptive evolution to selection pressures imposed by their herbivores and pathogens. Our study provided insight into the structural variation of chloroplast genomes, phylogenetic relationships, and adaptive evolution in Indigofera. These results will facilitate future studies on species identification, interspecific and intraspecific delimitation, adaptive evolution, and the phylogenetic relationships of the genus Indigofera.

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The chloroplast genome of Amygdalus L. (Rosaceae) reveals the phylogenetic relationship and divergence time

Cited by 21 publications

References 67 publications

Comparative chloroplast genome analysis of Ficus (Moraceae): Insight into adaptive evolution and mutational hotspot regions

Comparative chloroplast genome analysis of Ficus (Moraceae): Insight into adaptive evolution and mutational hotspot regions

Sequence Characteristics and Phylogenetic Analysis of the Artemisia argyi Chloroplast Genome

Phylogenomics and plastome evolution of Indigofera (Fabaceae)

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