Plastid genome evolution in leafless members of the orchid subfamily Orchidoideae, with a focus on Degranvillea dermaptera DOI
Craig F. Barrett, Matthew C. Pace,

Cameron W. Corbett

et al.

American Journal of Botany, Journal Year: 2024, Volume and Issue: 111(7)

Published: July 1, 2024

Abstract Premise Leafless, heterotrophic plants are prime examples of organismal modification, the genomic consequences which have received considerable interest. In particular, plastid genomes (plastomes) being sequenced at a high rate, allowing continual refinement conceptual models reductive evolution in heterotrophs. However, numerous sampling gaps exist, hindering ability to conduct comprehensive phylogenomic analyses these plants. Methods Using floral tissue from an herbarium specimen, we and analyzed plastome Degranvillea dermaptera , rarely collected, leafless orchid species South America about little is known, including its phylogenetic affinities. Results The most reduced those among subfamily Orchidoideae. it has lost majority genes found leafy autotrophic species, structurally rearranged, similar gene content plastomes orchids. We strong evidence for placement within subtribe Spiranthinae using that explicitly account heterotachy, or lineage‐specific evolutionary rate variation over time. further relaxed selection on several correlations substitution rates other “traits” members Conclusions Our findings advance knowledge relationships paths genome orchids, experienced more independent transitions heterotrophy than any plant family. This study demonstrates importance collections comparative genomics poorly known conservation concern.

Language: Английский

Phylogenomics and intergenomic conflict in a challenging orchid clade (Calypsoinae): monophyly of Corallorhiza, paraphyly of Oreorchis, and resurrection of Kitigorchis DOI
Craig F. Barrett, John V. Freudenstein, Samuel V. Skibicki

et al.

Botanical Journal of the Linnean Society, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 17, 2025

Abstract Heterotrophic plants are among the most recalcitrant from a systematics perspective because of reduced morphological and genomic features, often extreme substitution rate heterogeneity. The orchid subtribe Calypsoinae exemplifies this, containing several lineages that have lost leaves photosynthesis. In particular, relationships leafy Asian Oreorchis leafless American Corallorhiza been contentious. Here we used nuclear sequence capture to resolve within addressed monophyly Oreorchis, for which previous studies highlighted conflicting patterns or paraphyly, depending on data analysed. Nuclear analyses provided strong support monophyletic paraphyletic latter with two strongly supported clades. As in studies, plastid recovered assemblages both genera. Topology tests using rejected constrained topologies, further revealing cytonuclear conflict. Network-based revealed lack evidence hybridization, suggesting incomplete lineage sorting associated biological historical factors driven intergenomic Additionally, found loci identified as putatively holomycotrophic species functionally enriched organellar functions. study provides case resurrection Kitigorchis sister Corallorhiza, species, erythrochrysea indica, highlights challenges phylogenetics mycoheterotrophs.

Language: Английский

Citations

1
Tracking hidden dimensions of plant biogeography from herbaria DOI Creative Commons
Barnabas H. Daru

New Phytologist, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 14, 2025

Plants are diverse, but investigating their ecology and evolution in nature across geographic temporal scales to predict how species will respond global change is challenging. With breadth, herbarium data provide physical evidence of the existence a place time. The remarkable size collections along with growing digitization efforts around world possibility extracting functional traits from preserved plant specimens makes them invaluable resources for advancing our understanding changing distributions over time, biogeography, conserving communities. Here, I synthesize core aspects biogeography that can be gleaned herbaria distributions, attributes (functional biogeography), conservation globe. advocate collaborative, multisite, multispecies research harness full potential these while addressing inherent challenges using macroecological investigations. Ultimately, present untapped opportunities enable predictions species' responses inform effective planning.

Language: Английский

Citations

1
Unveiling a Meaningful Form of Cypripedium × ventricosum Sw. (Cypripedioideae, Orchidaceae) from Changbai Mountain, China: Insights from Morphological, Molecular, and Plastome Analyses DOI Creative Commons
Ying Li, Xi Lu, Shuang Li

et al.

Plants, Journal Year: 2025, Volume and Issue: 14(5), P. 772 - 772

Published: March 3, 2025

A Cypripedium plant was discovered in Wangqing County, Changbai Mountain, Jilin Province. This newly of not only inhabits the same natural habitat as calceolus L. and × ventricosum Sw. but also has a morphology intermediate between that C. ventricosum. Its dorsal sepals, petals, synsepal are similar to those calceolus, while color its lip is For purpose distinguishing from other plants, we provisionally named it W1. To further verify taxonomic status W1, introduced three identified forms conducted molecular biology analyses with The confirmed relationship W1 ventricosum, phylogenetic analysis nuclear region demonstrated close calceolus. Collectively, morphological evidence indicates product backcross Although shows differences typical can still be considered form We investigated chloroplast genome this determined total length 196,850 bp. contains 132 genes, including 87 protein-coding 37 tRNA 8 rRNA genes. By analyzing position study clarified relationships among taxa characteristics, laying foundation for research on orchid evolution species conservation.

Language: Английский

Citations

1
Phylogenomic insights into the historical biogeography, character-state evolution, and species diversification rates of Cypripedioideae (Orchidaceae) DOI
Min Liao, Junyi Zhang, Yu Feng

et al.

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: 199, P. 108138 - 108138

Published: July 6, 2024

Language: Английский

Citations

5
expowo: An R package for mining global plant diversity and distribution data DOI Creative Commons
Débora C. Zuanny, Bruno Vilela, Peter Moonlight

et al.

Applications in Plant Sciences, Journal Year: 2024, Volume and Issue: 12(6)

Published: July 30, 2024

Abstract Premise Data on plant distribution and diversity from natural history collections taxonomic databases are increasingly becoming available online as exemplified by the Royal Botanic Gardens, Kew's Plants of World Online (POWO) database. This growing accumulation biodiversity information requires an advance in bioinformatic tools for accessing processing massive data use downstream science. We present herein expowo, open‐source package that facilitates extracting using botanical POWO. Methods Results The expowo is implemented R designed to handle entire vascular tree life. It includes functions readily distill distributional about all families, genera, or species plants. outputs a complete list each genus any family, with associated original publication, synonyms, distribution, plots global maps richness at country levels, well graphs displaying species‐discovery curves nomenclatural changes over time. To demonstrate expowo's strengths producing easy‐to‐handle outputs, we also show empirical examples set biodiverse countries representative species‐rich ecologically important angiosperm families. Conclusions By harnessing accommodate varying levels programming proficiency, assist users who have limited expertise efficiently distilling specific sources graphics further interpretation biogeographic patterns.

Language: Английский

Citations

5
Progress in systematics and biogeography of Orchidaceae DOI Creative Commons
Y WANG, Hanchen Wang, CHAO YE

et al.

Plant Diversity, Journal Year: 2024, Volume and Issue: 46(4), P. 425 - 434

Published: May 16, 2024

Orchidaceae are one of the largest families angiosperms in terms species richness. In last decade, numerous studies have delved into reconstructing phylogenetic framework Orchidaceae, leveraging data from plastid, mitochondrial and nuclear sources. These provided new insights systematics, diversification biogeography establishing a robust foundation for future research. Nevertheless, pronounced controversies persist regarding precise placement certain lineages within these frameworks. To address discrepancies deepen our understanding structure we provide comprehensive overview analysis focusing on contentious groups since 2015, delving discussions underlying reasons observed topological conflicts. We also novel at subtribal level. Furthermore, examine tempo mode orchid diversity perspective historical biogeography, highlighting factors contributing to extensive speciation. Ultimately, delineate avenues research aimed enhancing phylogeny diversity.

Language: Английский

Citations

4
Evolution of Whirly1 in the angiosperms: sequence, splicing, and expression in a clade of early transitional mycoheterotrophic orchids DOI Creative Commons

Rachel M. Muti,

Craig F. Barrett, Brandon T. Sinn

et al.

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: June 28, 2024

The plastid-targeted transcription factor Whirly1 ( WHY1 ) has been implicated in chloroplast biogenesis, plastid genome stability, and fungal defense response, which together represent characteristics of interest for the study autotrophic losses across angiosperms. While gene loss nuclear genomes well studied mycoheterotrophic plants, evolution molecular mechanisms impacting stability is completely unknown. Here, we characterize four early transitional orchid species genus Corallorhiza by synthesizing results phylogenetic, transcriptomic, comparative genomic analyses with sequences sampled from 21 orders We found an increased number non-canonical isoforms assembled all but greenest species, including intron retention some isoforms. Within , phylotranscriptomic revealed presence tissue-specific differential expression only most photosynthetically capable a coincident increase fully species. Gene- codon-level tests selective regimes did not infer significant signal either relaxed selection or episodic diversifying so late-stage full orchids Epipogium aphyllum Gastrodia elata . Additionally, nucleotide substitutions that likely impact function such as nonsense mutations, were observed mycoheterotrophs. propose our findings suggest splicing changes may precede shifts inferred therefore does support primary role transition to mycoheterotrophy Orchidaceae. Taken together, this provides comprehensive view angiosperms date.

Language: Английский

Citations

4
Elevational patterns of orchid diversity in mid-subtropical mountain forests of eastern China DOI Creative Commons
Qinghua Zhan,

Haihong Liao,

Yuelong Liang

et al.

Global Ecology and Conservation, Journal Year: 2025, Volume and Issue: unknown, P. e03405 - e03405

Published: Jan. 1, 2025

Language: Английский

Citations

0
Factors Influencing Orchid Species Richness in the Central Balkans: The Importance of Belowground Organ Types DOI Creative Commons
Vladan Djordjević, Dmitar Lakušić, Ivan Novković

et al.

Plants, Journal Year: 2025, Volume and Issue: 14(3), P. 443 - 443

Published: Feb. 3, 2025

The Balkan Peninsula is considered one of the most important centres orchid diversity in Europe. However, patterns species richness Central Balkans have not been sufficiently studied so far. aim this study was, therefore, to identify and factors that influence spatial variation Balkans. For analyses, area was divided into 10 × km grid cells. environmental variables determined for each cell used analyses were altitude, bioclimatic variables, geological substrates habitat types. A random forest (RF) analysis predictors strongly associated with richness. In addition total number taxa, orchids three belowground organ types analysed separately: (a) rhizomatous orchids, (b) palmately lobed fusiform tubers (“palmate tuberous orchids”) (c) spherical or ovoid (“ovoid orchids”). Balkans, 54 subspecies recorded, are Tara, Zvijezda, Jadovnik Zlatar Mountains Ovčar-Kablar Gorge. general, two groups cells largest i.e., hotspots, stood out: (1) a large altitudinal range (2) occupied by gorges ravines. gradients influencing specific ranges, while climatic less important. affecting (Abieti-Fagenion, Ostryo-Carpinion orientalis Pinion nigrae forests), highlighting role heterogeneity. maximum percentage Abieti-Fagenion Vaccinio-Picetea forests minimum value mean temperature driest quarter determining palmate whereas xero-thermophilous (Ostryo-Carpinion orientalis, Asplenietea trichomanis nigrae) has greatest on orchids. These results confirm hypothesis concerning origin development underground organs emphasising best adapted cold humid conditions, ability grow habitats very warm dry conditions. This provides good basis better conservation planning underlines importance strategies as feature life history should be when studying diversity.

Language: Английский

Citations

0
Reintroduction of an epiphytic orchid: plant size matters DOI Creative Commons
Wei Zhang, Jiao Qin,

Qin‐Chang Liao

et al.

Global Ecology and Conservation, Journal Year: 2025, Volume and Issue: unknown, P. e03496 - e03496

Published: Feb. 1, 2025

Language: Английский

Citations

0