Dataset Information

Complete plastome sequencing from Toona (Meliaceae) and phylogenomic analyses within Sapindales.

ABSTRACT: Premise of the Study:Toona (Meliaceae, Sapindales) is a small genus of five species of trees native from southern and eastern Asia to New Guinea and Australia. Complete plastomes were sequenced for three Toona species to provide a basis for future plastome genetic studies in threatened species of Toona. In addition, plastome structural evolution and phylogenetic relationships across Sapindales were explored with a larger data set of 29 Sapindales plastomes (including members of six out of nine families). Methods:The plastomes were determined using the Illumina sequencing platform; the phylogenetic analyses were conducted using maximum likelihood by RAxML. Results:The lengths of three Toona plastomes range from 159,185 to 158,196 bp. A total of 113 unique genes were found in each plastome. Across Sapindales, plastome gene structure and content were largely conserved, with the exception of the contraction of the inverted repeat region to exclude ycf1 in some species of Rutaceae and Sapindaceae, and the movement of trnI-GAU and trnA-UGC to a position outside the inverted repeat region in some Rutaceae species. Discussion:The three Toona plastomes possess the typical structure of angiosperm plastomes. Phylogenomic analysis of Sapindales recovered a mostly strongly supported phylogeny of Sapindales, including most of the backbone relationships, with some improvements compared to previous targeted-gene analyses.

SUBMITTER: Lin N

PROVIDER: S-EPMC5947613 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

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Complete plastome sequencing from <i>Toona</i> (Meliaceae) and phylogenomic analyses within Sapindales.

Lin Nan N Moore Michael J MJ Deng Tao T Sun Hang H Yang Lin-Sen LS Sun Yan-Xia YX Wang Heng-Chang HC

Applications in plant sciences 20180427 4

<h4>Premise of the study</h4><i>Toona</i> (Meliaceae, Sapindales) is a small genus of five species of trees native from southern and eastern Asia to New Guinea and Australia. Complete plastomes were sequenced for three <i>Toona</i> species to provide a basis for future plastome genetic studies in threatened species of <i>Toona</i>. In addition, plastome structural evolution and phylogenetic relationships across Sapindales were explored with a larger data set of 29 Sapindales plastomes (including ...[more]

PMID: 30131882

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Project description:BackgroundToona is a critical genus in the Meliaceae, and the plants of this group are an asset for both restorative and restorative purposes, the most flexible of which are Toona sinensis and Toona ciliata. To concentrate on the advancement of mitochondrial(Mt) genome variety in T.sinensis and T.ciliata, the Mt genomes of the two species were sequenced in high throughput independently, after de novo assembly and annotation to construct a Mt genome map for comparison in genome structure. Find their repetitive sequences and analyze them in comparison with the chloroplast genome, along with Maximum-likelihood(ML) phylogenetic analysis with 16 other relatives.Results(1) T. sinensis and T.ciliata are both circular structures with lengths of 683482 bp and 68300 bp, respectively. They share a high degree of similarity in encoding genes and have AT preferences. All of them have the largest Phe concentration and are the most frequently used codons. (2) Both of their Mt genome are highly preserved in terms of structural and functional genes, while the main variability is reflected in the length of tRNA, the number of genes, and the value of RSCU. (3) T. siniensis and T. ciliata were detected to have 94 and 87 SSRs, respectively, of which mononucleotides accounted for the absolute proportion. Besides, the vast majority of their SSRs were found to be poly-A or poly-T. (4)10 and 11 migrating fragments were identified in the comparison with the chloroplast genome, respectively. (5) In the ML evolutionary tree, T.sinensis and T.ciliata clustered individually into a small branch with 100% support, reflecting two species of Toona are very similarly related to each other.ConclusionsThis research provides a basis for the exploitation of T.sinensis and T.ciliata in terms of medicinal, edible, and timber resources to avoid confusion; at the same time, it can explore the evolutionary relationship between the Toona and related species, which does not only have an important practical value, but also provides a theoretical basis for future hybrid breeding of forest trees, molecular markers, and evolutionary aspects of plants, which has great scientific significance.

Dataset Information

Complete plastome sequencing from Toona (Meliaceae) and phylogenomic analyses within Sapindales.

Publications

Complete plastome sequencing from <i>Toona</i> (Meliaceae) and phylogenomic analyses within Sapindales.

Similar Datasets

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