Comparative plastome analysis of Blumea, with implications for genome evolution and phylogeny of Asteroideae

Show full item record



Permalink

http://hdl.handle.net/10138/331765

Citation

Abdullah , Mehmood , F , Heidari , P , Ahmed , I & Poczai , P 2021 , ' Comparative plastome analysis of Blumea, with implications for genome evolution and phylogeny of Asteroideae ' , Ecology and Evolution , vol. 11 , no. 12 , pp. 7810-7826 . https://doi.org/10.1002/ece3.7614

Title: Comparative plastome analysis of Blumea, with implications for genome evolution and phylogeny of Asteroideae
Author: Abdullah,; Mehmood, Furrukh; Heidari, Parviz; Ahmed, Ibrar; Poczai, Péter
Other contributor: University of Helsinki, Botany

Date: 2021-06
Language: eng
Number of pages: 17
Belongs to series: Ecology and Evolution
ISSN: 2045-7758
DOI: https://doi.org/10.1002/ece3.7614
URI: http://hdl.handle.net/10138/331765
Abstract: The genus Blumea (Asteroideae, Asteraceae) comprises about 100 species, including herbs, shrubs, and small trees. Previous studies have been unable to resolve taxonomic issues and the phylogeny of the genus Blumea due to the low polymorphism of molecular markers. Therefore, suitable polymorphic regions need to be identified. Here, we de novo assembled plastomes of the three Blumea species B. oxyodonta, B. tenella, and B. balsamifera and compared them with 25 other species of Asteroideae after correction of annotations. These species have quadripartite plastomes with similar gene content and genome organization comprising 113 genes, including 80 protein-coding, 29 transfer RNA, and 4 ribosomal RNA genes. The contraction and expansion of inverted repeats also show high similarities among the species. The comparative analysis of codon usage, amino acid frequency, microsatellite repeats, oligonucleotide repeats, and transition and transversion substitutions has revealed high resemblance among the newly assembled species of Blumea. We identified 10 highly polymorphic regions with nucleotide diversity above 0.02, including rps16-trnQ, ycf1, ndhF-rpl32, rps15, petN-psbM, and rpl32-trnL, and they may be suitable for the development of robust, authentic, and cost-effective markers for bar coding and inference of the phylogeny of the genus Blumea. Among these highly polymorphic regions, five regions also co-occurred with oligonucleotide repeats and support use of repeats as a proxy for the identification of polymorphic loci. The phylogenetic analysis revealed a close relationship between Blumea and Pluchea within the tribe Inuleae. Our study supports a sister relationship between “Astereae and Anthemideae,” while Gnaphalieae roots these two tribes, whereas in a previous study a sister relationship was reported between “Senecioneae and Anthemideae” and “Astereae and Gnaphalieae” using nuclear genome sequences. The conflicting phylogenetic signals observed at the tribal level between chloroplast and nuclear genome data require further investigation.
Subject: 1181 Ecology, evolutionary biology
1184 Genetics, developmental biology, physiology
11831 Plant biology
Asteraceae
Asteroideae
barcode
Blumea
oligonucleotide repeat
plastome
polymorphic loci
TRANSFER-RNA GENES
CHLOROPLAST GENOMES
MATERNAL INHERITANCE
LEVEL PHYLOGENY
ASTERACEAE
SEQUENCE
DYNAMICS
DNA
ORGANIZATION
ALIGNMENT
Rights:


Files in this item

Total number of downloads: Loading...

Files Size Format View
cp_Blumea_Ecol_Evol_2021.pdf 3.061Mb PDF View/Open

This item appears in the following Collection(s)

Show full item record