Dataset Information

The complete chloroplast genome of Ampelopsis grossedentata (Hand.-Mazz.) W. T. Wang (Family: Vitaceae) and its phylogenetic analysis.

ABSTRACT: Ampelopsis grossedentata (Hand.-Mazz.) W. T. Wang is rich in flavonoids and also displays excellent pharmacological activities. The phylogenetic relationship between A. grossedentata and other related Vitaceae family members remains unclear. The chloroplast (cp) genome is a useful model for assessing genome evolution. In this study, we assembled the cp genome of A. grossedentata using the high-throughput Illumina pair-end sequencing data and characterized the genome to providing useful information for future genetic studies. The circular cp genome was 162,147 bp in size, including a large single-copy (LSC) region of 89,244 bp and a small single-copy (SSC) region of 18,439 bp, which were separated by two inverted repeat (IR) regions (27,232 bp each). A total of 135 genes were predicted, including 8 ribosomal RNAs (rRNAs), 37 transfer RNAs (tRNAs), and 90 protein-coding genes (PCGs). Furthermore, phylogenetic analysis revealed that A. grossedentata within Ampelopsis genus and formed a different clade from other three congeneric species. This study provides useful information for future genetic study of A. grossedentata.

SUBMITTER: Gu L

PROVIDER: S-EPMC7782978 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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The complete chloroplast genome of Ampelopsis grossedentata (Hand.-Mazz.) W. T. Wang (Family: Vitaceae) and its phylogenetic analysis.

Gu Lei L Zhang Ni N Feng Chun C Yi Yin Y Yu Zheng-Wen ZW

Mitochondrial DNA. Part B, Resources 20200611 3

Ampelopsis grossedentata (Hand.-Mazz.) W. T. Wang is rich in flavonoids and also displays excellent pharmacological activities. The phylogenetic relationship between A. grossedentata and other related Vitaceae family members remains unclear. The chloroplast (cp) genome is a useful model for assessing genome evolution. In this study, we assembled the cp genome of A. grossedentata using the high-throughput Illumina pair-end sequencing data and characterized the genome to provi ...[more]

PMID: 33457812

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Project description:Ampelopsis brevipedunculata is an economically important plant that belongs to the Vitaceae family of angiosperms. The phylogenetic placement of Vitaceae is still unresolved. Recent phylogenetic studies suggested that it should be placed in various alternative families including Caryophyllaceae, asteraceae, Saxifragaceae, Dilleniaceae, or with the rest of the rosid families. However, these analyses provided weak supportive results because they were based on only one of several genes. Accordingly, complete chloroplast genome sequences are required to resolve the phylogenetic relationships among angiosperms. Recent phylogenetic analyses based on the complete chloroplast genome sequence suggested strong support for the position of Vitaceae as the earliest diverging lineage of rosids and placed it as a sister to the remaining rosids. These studies also revealed relationships among several major lineages of angiosperms; however, they highlighted the significance of taxon sampling for obtaining accurate phylogenies. In the present study, we sequenced the complete chloroplast genome of A. brevipedunculata and used these data to assess the relationships among 32 angiosperms, including 18 taxa of rosids. The Ampelopsis chloroplast genome is 161,090 bp in length, and includes a pair of inverted repeats of 26,394 bp that are separated by small and large single copy regions of 19,036 bp and 89,266 bp, respectively. The gene content and order of Ampelopsis is identical to many other unrearranged angiosperm chloroplast genomes, including Vitis and tobacco. A phylogenetic tree constructed based on 70 protein-coding genes of 33 angiosperms showed that both Saxifragales and Vitaceae diverged from the rosid clade and formed two clades with 100% bootstrap value. The position of the Vitaceae is sister to Saxifragales, and both are the basal and earliest diverging lineages. Moreover, Saxifragales forms a sister clade to Vitaceae of rosids. Overall, the results of this study will contribute to better support of the evolution, molecular biology and genetic improvement of the plant Ampelopsis.

Project description:BackgroundThe Vitaceae (grape) is an economically important family of angiosperms whose phylogenetic placement is currently unresolved. Recent phylogenetic analyses based on one to several genes have suggested several alternative placements of this family, including sister to Caryophyllales, asterids, Saxifragales, Dilleniaceae or to rest of rosids, though support for these different results has been weak. There has been a recent interest in using complete chloroplast genome sequences for resolving phylogenetic relationships among angiosperms. These studies have clarified relationships among several major lineages but they have also emphasized the importance of taxon sampling and the effects of different phylogenetic methods for obtaining accurate phylogenies. We sequenced the complete chloroplast genome of Vitis vinifera and used these data to assess relationships among 27 angiosperms, including nine taxa of rosids.ResultsThe Vitis vinifera chloroplast genome is 160,928 bp in length, including a pair of inverted repeats of 26,358 bp that are separated by small and large single copy regions of 19,065 bp and 89,147 bp, respectively. The gene content and order of Vitis is identical to many other unrearranged angiosperm chloroplast genomes, including tobacco. Phylogenetic analyses using maximum parsimony and maximum likelihood were performed on DNA sequences of 61 protein-coding genes for two datasets with 28 or 29 taxa, including eight or nine taxa from four of the seven currently recognized major clades of rosids. Parsimony and likelihood phylogenies of both data sets provide strong support for the placement of Vitaceae as sister to the remaining rosids. However, the position of the Myrtales and support for the monophyly of the eurosid I clade differs between the two data sets and the two methods of analysis. In parsimony analyses, the inclusion of Gossypium is necessary to obtain trees that support the monophyly of the eurosid I clade. However, maximum likelihood analyses place Cucumis as sister to the Myrtales and therefore do not support the monophyly of the eurosid I clade.ConclusionPhylogenies based on DNA sequences from complete chloroplast genome sequences provide strong support for the position of the Vitaceae as the earliest diverging lineage of rosids. Our phylogenetic analyses support recent assertions that inadequate taxon sampling and incorrect model specification for concatenated multi-gene data sets can mislead phylogenetic inferences when using whole chloroplast genomes for phylogeny reconstruction.

Dataset Information

The complete chloroplast genome of Ampelopsis grossedentata (Hand.-Mazz.) W. T. Wang (Family: Vitaceae) and its phylogenetic analysis.

Publications

The complete chloroplast genome of <i>Ampelopsis grossedentata</i> (Hand.-Mazz.) W. T. Wang (Family: Vitaceae) and its phylogenetic analysis.

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