Plastid phylogenomics reveals evolutionary relationships in the mycoheterotrophic orchid genus Dipodium and provides insights into plastid gene degeneration.

Autor:	Goedderz S; Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia.; Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany., Clements MA; Centre for Australian National Biodiversity Research (joint venture between Parks Australia and CSIRO), Canberra, ACT, Australia., Bent SJ; Data61, Commonwealth Industrial and Scientific Research Organisation (CSIRO), Brisbane, QLD, Australia., Nicholls JA; Australian National Insect Collection, Commonwealth Industrial and Scientific Research Organisation (CSIRO), Canberra, ACT, Australia., Patel VS; National Research Collections Australia, Commonwealth Industrial and Scientific Research Organisation (CSIRO), Canberra, ACT, Australia., Crayn DM; Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia., Schlüter PM; Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany., Nargar K; Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia.; National Research Collections Australia, Commonwealth Industrial and Scientific Research Organisation (CSIRO), Canberra, ACT, Australia.
Jazyk:	angličtina
Zdroj:	Frontiers in plant science [Front Plant Sci] 2024 Jun 13; Vol. 15, pp. 1388537. Date of Electronic Publication: 2024 Jun 13 (Print Publication: 2024).
DOI:	10.3389/fpls.2024.1388537
Abstrakt:	The orchid genus Dipodium R.Br. (Epidendroideae) comprises leafy autotrophic and leafless mycoheterotrophic species, with the latter confined to sect. Dipodium . This study examined plastome degeneration in Dipodium in a phylogenomic and temporal context. Whole plastomes were reconstructed and annotated for 24 Dipodium samples representing 14 species and two putatively new species, encompassing over 80% of species diversity in sect. Dipodium . Phylogenomic analysis based on 68 plastid loci including a broad outgroup sampling across Orchidaceae found that sect. Leopardanthus is the sister lineage to sect. Dipodium. Dipodium ensifolium , the only leafy autotrophic species in sect. Dipodium , was found to be a sister to all leafless, mycoheterotrophic species, supporting a single evolutionary origin of mycoheterotrophy in the genus. Divergence-time estimations found that Dipodium arose ca. 33.3 Ma near the lower boundary of the Oligocene and that crown diversification commenced in the late Miocene, ca. 11.3 Ma. Mycoheterotrophy in the genus was estimated to have evolved in the late Miocene, ca. 7.3 Ma, in sect. Dipodium . The comparative assessment of plastome structure and gene degradation in Dipodium revealed that plastid ndh genes were pseudogenised or physically lost in all Dipodium species, including in leafy autotrophic species of both Dipodium sections. Levels of plastid ndh gene degradation were found to vary among species as well as within species, providing evidence of relaxed selection for retention of the NADH dehydrogenase complex within the genus. Dipodium exhibits an early stage of plastid genome degradation, as all species were found to have retained a full set of functional photosynthesis-related genes and housekeeping genes. This study provides important insights into plastid genome degradation along the transition from autotrophy to mycoheterotrophy in a phylogenomic and temporal context. Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. (Copyright © 2024 Goedderz, Clements, Bent, Nicholls, Patel, Crayn, Schlüter and Nargar.)
Databáze:	MEDLINE
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