Lycophyte plastid genomics: extreme variation in GC, gene and intron content and multiple inversions between a direct and inverted orientation of the rRNA repeat.
Isoetes (quillworts)
Lycopodiaceae (clubmosses)
Lycopodiophyta (lycophytes)
Selaginella (spikemosses)
evolutionary stasis
gene loss
inversion
plastid genome (plastome)
Journal
The New phytologist
ISSN: 1469-8137
Titre abrégé: New Phytol
Pays: England
ID NLM: 9882884
Informations de publication
Date de publication:
04 2019
04 2019
Historique:
received:
27
08
2018
accepted:
10
12
2018
pubmed:
18
12
2018
medline:
28
2
2020
entrez:
18
12
2018
Statut:
ppublish
Résumé
Lycophytes are a key group for understanding vascular plant evolution. Lycophyte plastomes are highly distinct, indicating a dynamic evolutionary history, but detailed evaluation is hindered by the limited availability of sequences. Eight diverse plastomes were sequenced to assess variation in structure and functional content across lycophytes. Lycopodiaceae plastomes have remained largely unchanged compared with the common ancestor of land plants, whereas plastome evolution in Isoetes and especially Selaginella is highly dynamic. Selaginella plastomes have the highest GC content and fewest genes and introns of any photosynthetic land plant. Uniquely, the canonical inverted repeat was converted into a direct repeat (DR) via large-scale inversion in some Selaginella species. Ancestral reconstruction identified additional putative transitions between an inverted and DR orientation in Selaginella and Isoetes plastomes. A DR orientation does not disrupt the activity of copy-dependent repair to suppress substitution rates within repeats. Lycophyte plastomes include the most archaic examples among vascular plants and the most reconfigured among land plants. These evolutionary trends correlate with the mitochondrial genome, suggesting shared underlying mechanisms. Copy-dependent repair for DR-localized genes indicates that recombination and gene conversion are not inhibited by the DR orientation. Gene relocation in lycophyte plastomes occurs via overlapping inversions rather than transposase/recombinase-mediated processes.
Identifiants
pubmed: 30556907
doi: 10.1111/nph.15650
pmc: PMC6590440
doi:
Substances chimiques
RNA, Ribosomal
0
Banques de données
GENBANK
['SRR2037123', 'AY660566', 'GU191333', 'HM173080', 'KX426071', 'AB197035', 'MH549637', 'MH549643', 'MK089531', 'KJ408574', 'KP099648', 'KP099647', 'KC117178', 'AB086179', 'KY126308', 'LC192146']
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1061-1075Subventions
Organisme : Field Museum
Pays : International
Organisme : University of Nebraska-Lincoln
ID : IC-2699
Pays : International
Organisme : China Scholarship Council
Pays : International
Organisme : University of Michigan
Pays : International
Informations de copyright
© 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.
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