Multi-tissue transcriptome analysis of two Begonia species reveals dynamic patterns of evolution in the chalcone synthase gene family.

Tytuł:: Multi-tissue transcriptome analysis of two Begonia species reveals dynamic patterns of evolution in the chalcone synthase gene family.
Autorzy:: Emelianova K; Royal Botanic Gardens Edinburgh, 20a Inverleith Row, Edinburgh, EH3 5LR, UK. .; Dementia Research Institute at the University of Edinburgh, Edinburgh, UK. .
Martínez Martínez A; Royal Botanic Gardens Edinburgh, 20a Inverleith Row, Edinburgh, EH3 5LR, UK.; School of Biological Sciences, University of Edinburgh, King's Buildings, Mayfield Rd, Edinburgh, EH9 3JU, UK.
Campos-Dominguez L; Royal Botanic Gardens Edinburgh, 20a Inverleith Row, Edinburgh, EH3 5LR, UK.; School of Biological Sciences, University of Edinburgh, King's Buildings, Mayfield Rd, Edinburgh, EH9 3JU, UK.
Kidner C; Royal Botanic Gardens Edinburgh, 20a Inverleith Row, Edinburgh, EH3 5LR, UK.; School of Biological Sciences, University of Edinburgh, King's Buildings, Mayfield Rd, Edinburgh, EH9 3JU, UK.
Źródło:: Scientific reports [Sci Rep] 2021 Sep 07; Vol. 11 (1), pp. 17773. Date of Electronic Publication: 2021 Sep 07.
Typ publikacji:: Comparative Study; Journal Article
Język:: English
Imprint Name(s):: Original Publication: London : Nature Publishing Group, copyright 2011-
MeSH Terms:: Biological Evolution*
Gene Duplication*
Transcriptome*
Acyltransferases/*genetics
Begoniaceae/*genetics
Plant Proteins/*genetics
Amino Acid Sequence ; Base Sequence ; Begoniaceae/classification ; Begoniaceae/metabolism ; Evolution, Molecular ; Gene Ontology ; Genetic Variation ; Genome, Plant ; Molecular Sequence Annotation ; Multigene Family ; Organ Specificity ; Phylogeny ; Plant Structures/metabolism ; RNA, Plant/biosynthesis ; RNA, Plant/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Species Specificity
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Substance Nomenclature:: 0 (Plant Proteins)
0 (RNA, Plant)
EC 2.3.- (Acyltransferases)
EC 2.3.1.74 (flavanone synthetase)
Entry Date(s):: Date Created: 20210908 Date Completed: 20211116 Latest Revision: 20230205
Update Code:: 20240105
PubMed Central ID:: PMC8423730
DOI:: 10.1038/s41598-021-96854-y
PMID:: 34493743
: Czasopismo naukowe

Pełny tekst

Begonia is an important horticultural plant group, as well as one of the most speciose Angiosperm genera, with over 2000 described species. Genus wide studies of genome size have shown that Begonia has a highly variable genome size, and analysis of paralog pairs has previously suggested that Begonia underwent a whole genome duplication. We address the contribution of gene duplication to the generation of diversity in Begonia using a multi-tissue RNA-seq approach. We chose to focus on chalcone synthase (CHS), a gene family having been shown to be involved in biotic and abiotic stress responses in other plant species, in particular its importance in maximising the use of variable light levels in tropical plants. We used RNA-seq to sample six tissues across two closely related but ecologically and morphologically divergent species, Begonia conchifolia and B. plebeja, yielding 17,012 and 19,969 annotated unigenes respectively. We identified the chalcone synthase gene family members in our Begonia study species, as well as in Hillebrandia sandwicensis, the monotypic sister genus to Begonia, Cucumis sativus, Arabidopsis thaliana, and Zea mays. Phylogenetic analysis suggested the CHS gene family has high duplicate turnover, all members of CHS identified in Begonia arising recently, after the divergence of Begonia and Cucumis. Expression profiles were similar within orthologous pairs, but we saw high inter-ortholog expression variation. Sequence analysis showed relaxed selective constraints on some ortholog pairs, with substitutions at conserved sites. Evidence of pseudogenisation and species specific duplication indicate that lineage specific differences are already beginning to accumulate since the divergence of our study species. We conclude that there is evidence for a role of gene duplication in generating diversity through sequence and expression divergence in Begonia.
(© 2021. The Author(s).)

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