| RRC ID |
81199
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| 著者 |
Feng K, Walker JF, Marx HE, Yang Y, Brockington SF, Moore MJ, Rabeler RK, Smith SA.
|
| タイトル |
The link between ancient whole-genome duplications and cold adaptations in the Caryophyllaceae.
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| ジャーナル |
Am J Bot
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| Abstract |
PREMISE:The Caryophyllaceae (the carnation family) have undergone multiple transitions into colder climates and convergence on cushion plant adaptation, indicating that they may provide a natural system for cold adaptation research. Previous research has suggested that putative ancient whole-genome duplications (WGDs) are correlated with niche shifts into colder climates across the Caryophyllales. Here, we explored the genomic changes potentially involved in one of these discovered shifts in the Caryophyllaceae.
METHODS:We constructed a data set combining 26 newly generated transcriptomes with 45 published transcriptomes, including 11 cushion plant species across seven genera. With this data set, we inferred a dated phylogeny for the Caryophyllaceae and mapped ancient WGDs and gene duplications onto the phylogeny. We also examined functional groups enriched for gene duplications related to the climatic shift.
RESULTS:The ASTRAL topology was mostly congruent with the current consensus of relationships within the family. We inferred 15 putative ancient WGDs in the family, including eight that have not been previously published. The oldest ancient WGD (ca. 64.4-56.7 million years ago), WGD1, was found to be associated with a shift into colder climates by previous research. Gene regions associated with ubiquitination were overrepresented in gene duplications retained after WGD1 and those convergently retained by cushion plants in Colobanthus and Eremogone, along with other functional annotations.
CONCLUSIONS:Gene family expansions induced by ancient WGDs may have contributed to the shifts to cold climatic niches in the Caryophyllaceae. Transcriptomic data are crucial resources that help unravel heterogeneity in deep-time evolutionary patterns in plants.
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| ページ |
e16350
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| 公開日 |
2024-6-2
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| DOI |
10.1002/ajb2.16350
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| 解説 |
BiodiC-J data were referenced.
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| PMID |
38825760
|
| MeSH |
Acclimatization / genetics
Adaptation, Physiological / genetics
Caryophyllaceae* / genetics
Cold Temperature*
Evolution, Molecular
Gene Duplication*
Genome, Plant*
Phylogeny*
Transcriptome
|
| IF |
3.038
|
| リソース情報 |
| GBIF |
Spermatophyte collection of Himeji City Science Museum
Plant specimens of Toyota City Nature Sanctuary
Plant specimens of Otaru Museum
Plant specimens of Komatsu City Museum
The 6-7th National Survey on the Natural Environment: Vegetation Survey
Vascular Plant Specimens of Yamagata Prefectural Museum
Vascular plant specimens of Omachi Alpine Museum
Vascular plant specimens of Akita Prefectural Museum
Herbarium, University Archives and Collections, Fukushima University, Japan (FKSE)
Angiospermatatophytina Collection of Saitama Museum of Natural History
Vascular Plant Collection of Natural History Museum and Institute, Chiba
Herbarium Specimens of Museum of Nature and Human Activities, Hyogo Pref., Japan
Ibaraki Nature Museum, Vascular Plants collection
Vascular plant specimens of National Museum of Nature and Science (TNS)
Herbarium Specimens of Tokushima Prefectural Museum, Japan
Plant Specimens of Kurashiki Museum of Natural History
Spermatophyta specimens of Iwate Prefectural Museum
Vascular Plants Collection of Sagamihara City Museum
Plant specimens in the Museum of Nature and Human Activities, Hyogo Prefecture, Japan
Plant specimens deposited in Osaka Museum of Natural History, Japan
Vascular Plant Specimens of Kochi Prefectural Makino Botanical Garden
Plant specimens of Kiritappu Wetland Center
Vascular Plant Specimen database of Kanagawa Prefectural Museum of Natural History
Gunma Museum of Natural History, Vascular Plant Specimen
Vascular plants collection of Hiratsuka City Museum
Plant specimens of Kushiro City Museum
Vascular plant specimens of Sugadaira Research Station, Mountain Science Center, University of Tsukuba
Herbarium of Shinshu University
Plant specimens of Parthenon Tama Museum (PTHM)
Plant specimens of Obihiro Centennial City Museum
Vascular plant specimens of Nagano Environmental Conservation Research Institute, Nagano Prefecture
Vascular plant specimens of Toyama Science Museum
Plant distribution data with photograph |
