Phylogenomics and the flowering plant tree of life

Journal of Integrative Plant Biology, Journal Year: 2022, Volume and Issue: 65(2), P. 299 - 323

Published: Nov. 23, 2022

Abstract The advances accelerated by next‐generation sequencing and long‐read technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of studies adopting hundreds thousands genes across wealth clades have emerged ushered phylogenetics evolution into new era. meantime, roadmap researchers when making decisions different approaches their phylogenomic research design is imminent. This review focuses on utility genomic data (from organelle genomes, both reduced representation whole‐genome sequencing) in evolutionary investigations, describes baseline methodology experimental analytical procedures, summarizes recent progress flowering phylogenomics at ordinal, familial, tribal, lower levels. We also discuss challenges, such as adverse impact orthology inference reconstruction raised from systematic errors, underlying biological factors, duplication, hybridization/introgression, incomplete lineage sorting, together suggesting that bifurcating tree may not be best model life. Finally, we promising avenues future studies.

Language: Английский

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Comprehensive phylogenetic analyses of Orchidaceae using nuclear genes and evolutionary insights into epiphytism

Journal of Integrative Plant Biology, Journal Year: 2023, Volume and Issue: 65(5), P. 1204 - 1225

Published: Feb. 4, 2023

Orchidaceae (with >28,000 orchid species) are one of the two largest plant families, with economically and ecologically important species, occupy global diverse niches primary distribution in rainforests. Among orchids, 70% grow on other plants as epiphytes; epiphytes contribute up to ~50% diversity rainforests provide food shelter for animals microbes, thereby contributing health these ecosystems. Orchids account over two-thirds vascular an excellent model studying evolution epiphytism. Extensive phylogenetic studies subgroups have ;been crucial understanding relationships among many lineages, although some uncertainties remain. For example, subfamily Epidendroideae nearly all epiphytic tribes subtribes still controversial, hampering evolutionary analyses Here we obtained 1,450 low-copy nuclear genes from 610 including 431 newly generated transcriptomes, used them reconstruction robust trees highly supported placements subtribes. We also generally well-supported 131 genera 437 species that were not sampled by previous plastid phylogenomic studies. Molecular clock estimated origin at ~132 million years ago (Ma) divergences most 52 29 Ma. Character supports least 14 parallel origins epiphytism; such was placed recent common ancestor ~95% orchids linked modern Ten occurrences rapid increase diversification rate detected within near after K-Pg boundary, ~80% diversity. This study provides a family-wide tree thus far new insights into epiphytism plants.

Language: Английский

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Comparative and phylogenetic analyses of six Kenya Polystachya (Orchidaceae) species based on the complete chloroplast genome sequences

BMC Plant Biology, Journal Year: 2022, Volume and Issue: 22(1)

Published: April 6, 2022

Abstract Background Polystachya Hook. is a large pantropical orchid genus (c. 240 species) distributed in Africa, southern Asia and the Americas, with center of diversity Africa. Previous studies on species this have not obtained complete chloroplast genomes, structures variations. Additionally, phylogenetic position Orchidaceae still controversial uncertain. Therefore, study, we sequenced plastomes six Kenya based genome skimming, subjected them to comparative genomic analysis, reconstructed relationships other species. Results The results exhibited that genomes had typical quadripartite structure conserved arrangement moderate divergence. ranged from 145,484 bp 149,274 length an almost similar GC content 36.9–37.0%. Gene annotation revealed 106–109 single-copy genes. In addition, 19 genes are duplicated inverted regions, 16 each possessd one or more introns. Although no structural variations were observed among plastomes, about 1 kb inversion was found modesta all 11 ndh lost pseudogenized. Comparative analysis overall sequence identity confirmed for both coding non-coding regions , SC exhibit higher variation than IRs. Furthermore, there various amplifications IR Most protein-coding these high degree codon preference. We screened out SSRs seven relatively highly variable loci. Moreover, 13 discovered significant positive selection. Phylogenetic showed formed monophyletic clade closely related tribe Vandeae. family inferred 85 sequences generally consistent previous robust. Conclusions Our study initial report species, elucidates characteristics filters can contribute development DNA markers use genetic variability evolutionary . strongly support part

Language: Английский

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A chromosome‐scale Gastrodia elata genome and large‐scale comparative genomic analysis indicate convergent evolution by gene loss in mycoheterotrophic and parasitic plants

The Plant Journal, Journal Year: 2021, Volume and Issue: 108(6), P. 1609 - 1623

Published: Oct. 15, 2021

Mycoheterotrophic and parasitic plants are heterotrophic parasitize on fungi plants, respectively, to obtain nutrients. Large-scale comparative genomics analysis has not been conducted in mycoheterotrophic or between these two groups of parasites. We assembled a chromosome-level genome the fully plant Gastrodia elata (Orchidaceae) performed genomic analyses genomes G. four orchids (initial mycoheterotrophs), three (Cuscuta australis, Striga asiatica, Sapria himalayana), 36 autotrophs from various angiosperm lineages. It was found that while hemiparasite S. asiatica initial orchids, approximately 4-5% conserved orthogroups were lost, C. australis both lost 10% orthogroups, indicating increased heterotrophy is positively associated with gene loss. Importantly, many genes essential for autotrophs, including those involved photosynthesis, circadian clock, flowering time regulation, immunity, nutrient uptake, root leaf development, convergently australis. The high-quality will facilitate future studies physiology, ecology, evolution our findings highlight critical role loss lifestyles.

Language: Английский

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Advances and prospects of orchid research and industrialization

Horticulture Research, Journal Year: 2022, Volume and Issue: 9

Published: Jan. 1, 2022

Orchidaceae is one of the largest, most diverse families in angiosperms with significant ecological and economical values. Orchids have long fascinated scientists by their complex life histories, exquisite floral morphology pollination syndromes that exhibit exclusive specializations, more than any other plants on Earth. These intrinsic factors together human influences also make it a keystone group biodiversity conservation. The advent sequencing technologies transgenic techniques represents quantum leap orchid research, enabling molecular approaches to be employed resolve historically interesting puzzles basic applied biology. To date, 16 different genomes covering four subfamilies (Apostasioideae, Vanilloideae, Epidendroideae, Orchidoideae) been released. genome projects given rise massive data greatly empowers studies pertaining key innovations evolutionary mechanisms for breadth species. extensive exploration transcriptomics, comparative genomics, recent advances gene engineering linked important traits orchids multiplicity regulating networks, providing great potential genetic enhancement improvement. In this review, we summarize progress achievement fundamental research industrialized application particular focus tools, future prospects breeding post-genomic comprehensive assemblage state art knowledge industrialization.

Language: Английский

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Plastid phylogenomics provides new insights into the systematics, diversification, and biogeography of Cymbidium (Orchidaceae)

Plant Diversity, Journal Year: 2024, Volume and Issue: 46(4), P. 448 - 461

Published: March 12, 2024

Cymbidium (Orchidaceae: Epidendroideae), with around 60 species, is widely-distributed across Southeast Asia, providing a nice system for studying the processes that underlie patterns of biodiversity in region. However, phylogenetic relationships have not been well resolved, hampering investigations species diversification and biogeographical history this genus. In study, we construct plastome phylogeny 56 four well-resolved major clades, which provides framework rate analyses. Molecular dating analyses show likely originated region spanning northern Indo-Burma to eastern Himalayas during early Miocene (∼21.10 Ma). It then rapidly diversified into clades East Asia within approximately million years middle Miocene. spp. migration adjacent regions (Borneo, Philippines, Sulawesi) primarily occurred Pliocene-Pleistocene period. Our indicate net has decreased since its origin, positively associated changes temperature monsoon intensity. Favorable hydrothermal conditions brought by intensification possibly contributed initial rapid diversification, after was reduced cooling climate The transition from epiphytic terrestrial habits may enabled adaptation cooler environments colonization niches, yet without significant effect on rates. This study new insights how activity affected dynamics plants Asia.

Language: Английский

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Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

Scientific Reports, Journal Year: 2021, Volume and Issue: 11(1)

Published: March 25, 2021

Abstract Recent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between subfamilies of Orchidaceae and most tribes. However, uncertainty remains within several subtribes genera for which phylogenetic not ever been tested in a context. To address these knowledge-gaps, we here provide extensively sampled analysis orchid family to date, 78 coding genes representing 264 species, 117 genera, 18 tribes 28 subtribes. Divergence times are also provided as inferred from strict relaxed molecular clocks birth–death tree models. Our taxon sampling includes 51 newly sequenced genomes produced by genome skimming approach. We focus our efforts previously unplaced clades Cymbidieae Epidendreae. results confirmed recovered previous studies, were with maximum support (209 262 branches). first time clear placement Codonorchideae subfamily Orchidoideae, Podochilieae Collabieae Epidendroideae. identify that persistently problematic across multiple regardless different details genomic datasets used reconstructions. study provides an expanded, robust temporal framework paves way biogeographical macroevolutionary studies.

Language: Английский

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Hundreds of nuclear and plastid loci yield novel insights into orchid relationships

American Journal of Botany, Journal Year: 2021, Volume and Issue: 108(7), P. 1166 - 1180

Published: July 1, 2021

PREMISE The inference of evolutionary relationships in the species‐rich family Orchidaceae has hitherto relied heavily on plastid DNA sequences and limited taxon sampling. Previous studies have provided a robust phylogenetic framework, which was used to classify orchids investigate drivers orchid diversification. However, extent based genome is congruent with nuclear been only poorly assessed. METHODS We inferred higher‐level likelihood ASTRAL analyses 294 low‐copy genes sequenced using Angiosperms353 universal probe set for 75 species (representing 69 genera, 16 tribes, 24 subtribes) concatenated analysis 78 264 (117 18 28 subtribes). compared informativeness support hypotheses. RESULTS Phylogenetic data sets provides well‐supported that are highly between analyses. Comparisons gene trees supermatrix tree showed mostly congruent, but revealed instances strongly supported incongruence both shallow deep time. individual general better than most genes. CONCLUSIONS Our study first phylogenomic framework an assessment intragenomic discordance, plastid‐nuclear incongruence, across family. results also demonstrate what long known rarely thoroughly documented: can contain discordances, this must be reconciled prior interpretation studies, such as taxonomy, biogeography, character evolution.

Language: Английский

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Complete chloroplast genome structural characterization of two Phalaenopsis (Orchidaceae) species and comparative analysis with their alliance

BMC Genomics, Journal Year: 2023, Volume and Issue: 24(1)

Published: June 27, 2023

The taxonomy and infrageneric delimitation of Phalaenopsis Blume has been significantly disputed due to some overlapping morphological features between species related, which needed further evidence for clarification. structural characterization complete chloroplast genomes P. storbatiana wilsonii were analyzed compared with those related taxa provide a better understanding their genomic information on phylogeny.It was shown that had typical quadripartite structure conserved genome arrangements moderate divergence. 145,885 bp 145,445 in length, respectively, shared similar GC content 36.8%. Gene annotations two revealed 109 single-copy genes consistently. In addition, 20 duplicated the inverted regions, 16 each possessed one or more introns, five ndh (NA (D)H dehydrogenase) observed both. Comparative analysis total cp other six confirmed stable sequence identity coding non-coding regions higher variation SC than IR regions. Most protein-coding high degree codon preference. Moreover, 45 discovered positive selection. However, different amplifications these eight species. Phylogenetic based CDS from 60 representing main clades Orchidaceae indicated including stobartiana formed monophyletic clade bootstrap nested tribe Vandeae Epidendroideae, consistent previous studies.The results could insight into plastome evolution phylogenetic relationships Phalaenopsis.

Language: Английский

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Phylogenomics and morphological evolution of the mega-diverse genus Artemisia (Asteraceae: Anthemideae): implications for its circumscription and infrageneric taxonomy

Annals of Botany, Journal Year: 2023, Volume and Issue: 131(5), P. 867 - 883

Published: March 28, 2023

Abstract Background and Aims Artemisia is a mega-diverse genus consisting of ~400 species. Despite its medicinal importance ecological significance, well-resolved phylogeny for global Artemisia, natural generic delimitation infrageneric taxonomy remain missing, owing to the obstructions from limited taxon sampling insufficient information on DNA markers. Its morphological characters, such as capitulum, life form leaf, show marked variations are widely used in taxonomy. However, their evolution within poorly understood. Here, we aimed reconstruct via phylogenomic approach, infer evolutionary patterns key characters update circumscription Methods We sampled 228 species (258 samples) allies both fresh herbarium collections, covering all subgenera main geographical areas, conducted analysis based nuclear single nucleotide polymorphisms (SNPs) obtained genome skimming data. Based phylogenetic framework, inferred possible six previous Key Results The Kaschgaria was revealed be nested with strong support. A eight highly supported clades recovered, two which were identified first time. Most previously recognized not monophyletic. Evolutionary inferences showed that different states these originated independently more than once. Conclusions enlarged include Kaschgaria. traditionally do match new tree. They experienced complex history thought. propose revised newly circumscribed accommodate results.

Language: Английский

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