Tight association of genome rearrangements with gene expression in conifer plastomes.
Conifer
Plastid transcriptome
Plastomic rearrangement
RNA-editing
Strand-specific RNAseq
Journal
BMC plant biology
ISSN: 1471-2229
Titre abrégé: BMC Plant Biol
Pays: England
ID NLM: 100967807
Informations de publication
Date de publication:
08 Jan 2021
08 Jan 2021
Historique:
received:
09
10
2020
accepted:
20
12
2020
entrez:
9
1
2021
pubmed:
10
1
2021
medline:
4
5
2021
Statut:
epublish
Résumé
Our understanding of plastid transcriptomes is limited to a few model plants whose plastid genomes (plastomes) have a highly conserved gene order. Consequently, little is known about how gene expression changes in response to genomic rearrangements in plastids. This is particularly important in the highly rearranged conifer plastomes. We sequenced and reported the plastomes and plastid transcriptomes of six conifer species, representing all six extant families. Strand-specific RNAseq data show a nearly full transcription of both plastomic strands and detect C-to-U RNA-editing sites at both sense and antisense transcripts. We demonstrate that the expression of plastid coding genes is strongly functionally dependent among conifer species. However, the strength of this association declines as the number of plastomic rearrangements increases. This finding indicates that plastomic rearrangement influences gene expression. Our data provide the first line of evidence that plastomic rearrangements not only complicate the plastomic architecture but also drive the dynamics of plastid transcriptomes in conifers.
Sections du résumé
BACKGROUND
BACKGROUND
Our understanding of plastid transcriptomes is limited to a few model plants whose plastid genomes (plastomes) have a highly conserved gene order. Consequently, little is known about how gene expression changes in response to genomic rearrangements in plastids. This is particularly important in the highly rearranged conifer plastomes.
RESULTS
RESULTS
We sequenced and reported the plastomes and plastid transcriptomes of six conifer species, representing all six extant families. Strand-specific RNAseq data show a nearly full transcription of both plastomic strands and detect C-to-U RNA-editing sites at both sense and antisense transcripts. We demonstrate that the expression of plastid coding genes is strongly functionally dependent among conifer species. However, the strength of this association declines as the number of plastomic rearrangements increases. This finding indicates that plastomic rearrangement influences gene expression.
CONCLUSIONS
CONCLUSIONS
Our data provide the first line of evidence that plastomic rearrangements not only complicate the plastomic architecture but also drive the dynamics of plastid transcriptomes in conifers.
Identifiants
pubmed: 33419387
doi: 10.1186/s12870-020-02809-2
pii: 10.1186/s12870-020-02809-2
pmc: PMC7796615
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
33Subventions
Organisme : Ministry of Science and Technology, Taiwan
ID : MOST 106-2311-B-001-005
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