Phylogenetic reconstruction and divergence time estimation of Blumea DC. (Asteraceae: Inuleae) in China based on nrDNA ITS and cpDNA trnL-F sequences

Zhang, Yingbo; Yuan, Yuan; Pang, Yuxin; Yu, Fu-Lai; Wang, Dan; Hu, Xuan; Chen, Xiao-lu; Guan, Lingliang; Yuan, Chao

doi:10.1101/497073

Cited by 4 publications

(13 citation statements)

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“…The alignments were used for phylogenetic analysis. After that, according to the method described by Xie et al [55] and Zhang et al [56], we used four methods to construct phylogenetic trees: NJ method, MP method, BI method and ML method. Coffea canephora and Coffea arabica were selected as the outgroup.…”

Section: Phylogenetic Analysis Of Camelliamentioning

confidence: 99%

Exploring the evolutionary characteristics between cultivated tea and its wild relatives using complete chloroplast genomes

Peng

Zhao

Meng

et al. 2020

Preprint

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Background: Cultivated tea is one of the most important economic and ecological trees distributed worldwide. Cultivated tea suffer from long-term targeted selection of traits and overexploitation of habitats by human beings, which may have changed its genetic structure. The chloroplast is an organelle with a conserved cyclic genomic structure, and it can help us better understand the evolutionary relationship of Camellia plants. Results: We conducted comparative and evolutionary analyses on cultivated tea and wild tea, and we detected the evolutionary characteristics of cultivated tea. The chloroplast genome sizes of cultivated tea were slightly different, ranging from 157,025 bp to 157,100 bp. In addition, the cultivated species were more conserved than the wild species, in terms of the genome length, gene number, gene arrangement and GC content. However, comparing Camellia sinensis var. sinensis and Camellia sinensis var. assamica with their cultivars, the IR length variation was approximately 20 bp and 30 bp, respectively. The nucleotide diversity of 14 sequences in cultivated tea was higher than that in wild tea. Detailed analysis on the genomic variation and evolution of Camellia sinensis var. sinensis cultivars revealed 67 single nucleotide polymorphisms (SNPs), 46 insertions/deletions (indels), and 16 protein coding genes with nucleotide substitutions, while Camellia sinensis var. assamica cultivars revealed 4 indels. In cultivated tea, the most variable gene was ycf1 . The largest number of nucleotide substitutions, five amino acids exhibited site-specific selection, and a 9 bp sequence insertion were found in the Camellia sinensis var. sinensis cultivars. In addition, phylogenetic relationship in the ycf1 tree suggested that the ycf1 gene has evolved in cultivated tea. Because C. sinensis var. sinensis and its cultivated species were not tightly clustered. Conclusions: The cultivated species were more conserved than the wild species in terms of architecture and linear sequence order. The variation of the chloroplast genome in cultivated tea was mainly manifested in the nucleotide polymorphisms and sequence insertions. The ycf1 gene played an important role in the adaptive evolution of cultivated tea. These results provided evidence regarding the influence of human activities on tea.

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Section: Phylogenetic Analysis Of Camelliamentioning

confidence: 99%

Exploring the evolutionary characteristics between cultivated tea and its wild relatives using complete chloroplast genomes

Peng

Zhao

Meng

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…The alignments were used for phylogenetic analysis. According to the method described by Xie et al [53] and Zhang et al [54], we used four methods to construct phylogenetic trees, that were the NJ method, the MP method, the BI method and the ML method. Coffea canephora and Coffea arabica were selected as the outgroup.…”

Section: Phylogenetic Analysis Of Camelliamentioning

confidence: 99%

Exploring evolution characteristic between cultivated tea and its wild relatives using complete chloroplast genomes

Peng

Zhao

Meng

et al. 2020

Preprint

View full text Add to dashboard Cite

Abstract Background: The cultivated tea is one of the most important economic and ecological trees distributing worldwide. The cultivated tea suffered from long-term targeted selection of traits and overexploitation of habitats by human beings, which may change the genetic structure. Chloroplast is an organelle with a conserved cyclic structure, and can help us better understand the evolutionary relationship of Camellia plants.Results: The study conducted comparative analysis and evolution analysis between cultivated tea and wild tea, and detected the evolution characteristic in cultivated tea. Chloroplast genome sizes of cultivated tea were slightly different, ranged from 157,025 bp to 157,085 bp. These cultivated species were more conservative than wild species, in terms of the genome length, genes number, genes arrangement and GC contents. However, the IRs length of cultivated species was about 20 bp shorter than that of C. sinensis var. sisnensis. We also found that the nucleotide diversity of 14 sequences in cultivated tea was higher than that of wild tea. These results provided the evidence on the variation of chloroplast genomes of cultivated tea. Detail analysis on the chloroplast genome variation and evolution of cultivated tea showed that 67 SNPs and 46 indels and 16 protein coding genes had nucleotide substitutions. The most comment variation gene was ycf1. It has the largest number of nucleotide substitutions. At the same time, in ycf1, five amino acid sites were exhibiting site-specific selection, and a 9 bp sequence insertion was found in the C. sinensis cultivar. Anhua. The phylogenetic tree constructed by ycf1 sequence shows that two cultivated tea were not completely clustered, and the evolutionary relationship between C. sinensis var. sisnensis and C. sinensis cultivar. Longjing is closer than that of C. sinensis cultivar. Anhua.Conclusions: The cultivated species were more conservative than wild species in terms of architecture and linear sequence order. The variation of chloroplast genome of cultivated tea was mainly manifested in the nucleotide polymorphism of some sequences. The ycf1 gene played an important role in the adaptive evolution of cultivated tea. These results provided evidence regarding the influence of human activities on tea.

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“…Previous phylogenetic studies had revealed that Blumea is a sister group of the genus Caesulia Roxb. (Anderberg et al 2005 ; Pornpongrungrueng et al 2007 ; Zhang et al 2019 ). Combining evolutionary information of the ITS, trnL-trnF , and trnH-psbA regions from 30 Blumea species, Pornpongrungrueng et al ( 2007 , 2009 ) were the first to examine the infrageneric relationships of Blumea and identified three clades in the genus–– B. lacera clade, B. densiflora clade, and B. balsamifera clade.…”

Section: Introductionmentioning

confidence: 99%

“…Their phylogeny showed that the relationships among the three clades were unresolved and pointed out that several taxa were not monophyletic. Zhang et al ( 2019 ) investigated the infrageneric relationships of 22 Chinese Blumea taxa with the ITS and trnL-trnF regions, recognized two clades. The clade I, which contained B. densiflora clade and B. balsamifera clade recognized by Pornpongrungrueng et al ( 2007 , 2009 ), however, had low supports in Zhang et al ( 2019 ) phylogenies.…”

Section: Introductionmentioning

confidence: 99%

“…Zhang et al ( 2019 ) investigated the infrageneric relationships of 22 Chinese Blumea taxa with the ITS and trnL-trnF regions, recognized two clades. The clade I, which contained B. densiflora clade and B. balsamifera clade recognized by Pornpongrungrueng et al ( 2007 , 2009 ), however, had low supports in Zhang et al ( 2019 ) phylogenies. The clade II was equal to B. lacera clade in Pornpongrungrueng et al ( 2007 , 2009 ).…”

Section: Introductionmentioning

confidence: 99%

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Blumea chishangensis sp. nov. (Asteraceae: Inuleae) from Taiwan and new insights into the phylogeny of Blumea

Chung

Huang

Chen³

et al. 2022

Bot Stud

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Background Blumea plants are widely distributed in the tropical areas of Asia, Africa, and Australia, especially tropical Asia. Limited studies left the taxonomy and infrageneric phylogeny of Blumea insubstantial. Here, a new species, Blumea chishangensis S. W. Chung, Z. H. Chen, S. H. Liu & W. J. Huang, from Taiwan is described, and an extended phylogeny is reconstructed to provide new perceptions of Blumea evolution. Results The new species is distinguished from B. hieraciifolia by the following features: leaf blade sparsely pilose or glabrescent (vs. silky villous), the leaves margins regularly remote mucronulate (vs. double serrate or dentate), capitula pedicelled (vs. capitula sessile or subsessile), and leaves basal rosette or sub-basal rosette and a few cauline (vs. mostly cauline). Phylogenetic analysis based on the ITS, trnL-trnF, and trnH-psbA regions places the new species in the subclade II in B. lacera clade and shows a close relationship with B. axillaris and B. oxyodonta. A key to Blumea species in Taiwan and the studied species in the subclade II is provided. Moreover, the evolutionary inferences of B. conspicua, B. linearis, and B. sinuata are first reported here. The paraphyly of B. formosana and B. sinuata are also revealed for the first time. Conclusions Both morphological and molecular data support that B. chishangensis is a new species. Our phylogeny highlights the need for further taxonomic and evolutionary studies on Blumea.

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Phylogenetic reconstruction and divergence time estimation of Blumea DC. (Asteraceae: Inuleae) in China based on nrDNA ITS and cpDNA trnL-F sequences

Abstract: 1 5

Cited by 4 publications

References 40 publications

Exploring the evolutionary characteristics between cultivated tea and its wild relatives using complete chloroplast genomes

Exploring the evolutionary characteristics between cultivated tea and its wild relatives using complete chloroplast genomes

Exploring evolution characteristic between cultivated tea and its wild relatives using complete chloroplast genomes

Blumea chishangensis sp. nov. (Asteraceae: Inuleae) from Taiwan and new insights into the phylogeny of Blumea

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