RRC ID 82406
Author Wu W, Guo L, Yin L, Cai B, Li J, Li X, Yang J, Zhou H, Tao Z, Li Y.
Title Genomic convergence in terrestrial root plants through tandem duplication in response to soil microbial pressures.
Journal Cell Rep
Abstract Despite increasing reports of convergent adaptation, evidence for genomic convergence across diverse species worldwide is lacking. Here, our study of 205 Archaeplastida genomes reveals evidence of genomic convergence through tandem duplication (TD) across different lineages of root plants despite their genomic diversity. TD-derived genes, notably prevalent in trees with developed root systems embedded in soil, are enriched in enzymatic catalysis and biotic stress responses, suggesting adaptations to environmental pressures. Correlation analyses suggest that many factors, particularly those related to soil microbial pressures, are significantly associated with TD dynamics. Conversely, flora transitioned to aquatic, parasitic, halophytic, or carnivorous lifestyles-reducing their interaction with soil microbes-exhibit a consistent decline in TD frequency. This trend is further corroborated in mangroves that independently adapted to hypersaline intertidal soils, characterized by diminished microbial activity. Our findings propose TD-driven genomic convergence as a widespread adaptation to soil microbial pressures among terrestrial root plants.
Volume 43(10)
Pages 114786
Published 2024-9-26
DOI 10.1016/j.celrep.2024.114786
PII S2211-1247(24)01137-9
PMID 39331502
MeSH Gene Duplication* Genome, Plant Genomics Phylogeny Plant Roots* / genetics Plant Roots* / microbiology Soil Microbiology* Tandem Repeat Sequences / genetics
Resource
GBIF Fern (Pteridophyta) specimens of Toyama Science Museum Plant specimens of Ishikawa Museum of Natural History Pteridophyte specimens of Okinawa Prefectural Museum & Art Museum Bryophyte specimens of Kanagawa Prefectural Museum of Natural History Plant Specimens of The Cattle Museum Long-term fauna and flora records of the experimental forests of the Forest Research Station of Hokkaido University, Japan Spermatophyte collection of Himeji City Science Museum Plant specimens of Toyota City Nature Sanctuary Plant specimens of Tochigi Prefectural Museum Plant specimens of Nasunogahara Museum Ferns and Lycophytes Specimens of Kawasaki Municipal Science Museum Herbarium Specimens of The Kagoshima University Museum (KAG) Japanese Woody Plants Survey data of algal beds on the Monitoring sites 1000 project, BDCJ Asia-Pacific Dataset Vascular plant specimens of the herbarium of the Tohoku University (TUS) Spermatophyta Specimens of Kawasaki Municipal Science Museum Botanical collection of Gifu Prefecture Museum Microalgal collection of National Museum of Nature and Science (TNS) Gunma Museum of Natural History, Bryophyta Specimen Plant Specimen Database of Tama Forest Science Garden, Forestry and Forest Products Research Institute, Japan Plant specimens of Otaru Museum Kelp Dataset The south coast survey of Hatakejima Islands from 1969 Survey data of seagrass beds on the Monitoring sites 1000 project, BDCJ Plant specimens of Komatsu City Museum Biological Resource Center, Department of Biotechnology, National Institute of Technology and Evaluation Seaweed (Plantae) Collection of the Seto Marine Biological Laboratory, Kyoto University Algae collection of Museum of Natural and Environmental History, Shizuoka Vascular plant specimens of the Kagoshima Prefectural Museum Bryophyte specimens of Nagano Environmental Conservation Research Institute, Nagano Prefecture Paleobotany collection of National Museum of Nature and Science Plant specimens of Horaiji-san Museum of Natural History Toji K. collection The 6-7th National Survey on the Natural Environment: Vegetation Survey Herbaceous and arboreous plants list on the Komaba Campus of University of Tokyo, Japan Vascular Plant Specimens of Yamagata Prefectural Museum Nagoya-Plants Vascular plant specimens of Omachi Alpine Museum Plant specimens of Natural History Museum, Kishiwada City Vascular Plants Specimens of Ehime Prefectural Science Museum Plant Specimens collections of the Kyushu University Museum Bryophyte specimens of Iwate Prefectural Museum Vascular plant specimens of Akita Prefectural Museum Vascular plants database of Atsugi City Museum Herbarium, University Archives and Collections, Fukushima University, Japan (FKSE) Bryophytes specimens of Okinawa Prefectural Museum & Art Museum Angiospermatatophytina Collection of Saitama Museum of Natural History Bryophyta Collection of Saitama Museum of Natural History Vascular plant specimens of Iida City Museum AIS Wildtype Populations of Arabidopsis Plankton&BenthosResearch Plant specimens of Oiso Municipal Museum Herbarium of Hokkaido University Museum (SAPS) Bryophyte Collection of Natural History Museum and Institute, Chiba Vascular Plant Collection of Natural History Museum and Institute, Chiba Bryophytes specimens of Akita Prefectural Museum Herbarium Specimens of Museum of Nature and Human Activities, Hyogo Pref., Japan Pteridophyta specimens of Iwate Prefectural Museum Pteridophyta collection of Museum of Natural and Environmental History, Shizuoka Spermatophyta collection of Museum of Natural and Environmental History, Shizuoka Ibaraki Nature Museum, Bryophyta collection Ibaraki Nature Museum, Algae collection Ibaraki Nature Museum, Vascular Plants collection Kitami Region Museum of Science History and Art(KIRM) Lichen specimens of National Museum of Nature and Science (TNS) Bryophyte specimens of National Museum of Nature and Science (TNS) Macroalgal collection of National Museum of Nature and Science (TNS) Vascular plant specimens of National Museum of Nature and Science (TNS) Plant Specimens of Kurashiki Museum of Natural History Herbarium Specimens of Tokushima Prefectural Museum, Japan Herbarium of Kitakyushu Museum of Natural History and Human History Bryophyte specimens database of Mr. Tsutomu Kodama collection Plant Specimens of Lake Biwa Museum 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 of Taga Town Museum, Shiga Pref., Japan Plant specimens deposited in Osaka Museum of Natural History, Japan Vascular Plant Specimens of Kochi Prefectural Makino Botanical Garden Plant Specimens of Wakayama Prefectural Museum of Natural History Plant Specimens of The Shimane Nature Museum of Mt. Sanbe Bryophyte specimens of The Nagoya University Museum Plant specimens of Kiritappu Wetland Center Fossil specimens of Tochigi Prefectural Museum Coastal Ecosystem Monitoring in the Tsugaru strait side of Shimokita 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 Vascular Plant Specimens of the URO Herbarium (Faculty of Education, University of the Ryukyus) Plant specimens of Kushiro City Museum Algae specimens of Kanagawa Prefectural Museum of Natural History Monitoring records of plant species in the Hakone region of Fuji-Hakone-Izu National Park, Japan, 2001-2010 Plant specimens of Horaiji-san Museum of Natural History Kichi T. collection A dataset for vascular plant diversity monitoring for the natural World Heritage site on Amami-Oshima Island, Tokunoshima Island, and the northern Okinawa Island Spermatophytes collection of Okinawa Prefectural Museum & Art Museum Fossil Specimens of Ibaraki Nature Museum Vascular Plant Specimens of the RYU Herbarium (Faculty of Science, University of the Ryukyus) Plant specimens of Bihoro Museum Microbial Culture Collection, National Institute for Environmental Studies Plant specimens of Mie Prefectural Museum Herbarium Specimens of Bonin and Ryukyu Islands Vascular plant specimens of Sugadaira Research Station, Mountain Science Center, University of Tsukuba The 2nd and 3rd National Survey on the Natural Environment: Vegetation Survey (common species) The 2nd and 3rd National Survey on the Natural Environment: Vegetation Survey (rare species) Bryophyte specimens of Toyama Science Museum 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 Plant Observation Records of Japan Botanical Specimens of Kaizuka City Museum of Natural History (KCMN) Tracheophyta collection of Biodiversity Center of Japan, Ministry of the Environment Moss specimens of Kushiro City Museum Vascular plant specimens of The Shirakami Research Center for Environmental Sciences, Hirosaki University Vascular plant specimens of Aomori City Forestry Museum Asahikawa Educational College herbarium Plant specimens of the Museum of Yamagata University Plant specimens of Toyota City Nature Sanctuary (from non-museum circle) Vascular plant specimens of Toyama Science Museum Plant specimens of Takatsuki Nature Museum (Aquapia Akutagawa) Plant distribution data with photograph