Complete chloroplast genomes provide insights into evolution and phylogeny of Zingiber (Zingiberaceae)

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

Published: Jan. 18, 2023

The genus Zingiber of the Zingiberaceae is distributed in tropical, subtropical, and Far East Asia. This contains about 100-150 species, with many species valued as important agricultural, medicinal horticultural resources. However, genomic resources suitable molecular markers for identification are currently sparse.We conducted comparative genomics phylogenetic analyses on species. chloroplast genome (size range 162,507-163,711 bp) possess typical quadripartite structures that consist a large single copy (LSC, 86,986-88,200 bp), small (SSC, 15,498-15,891 pair inverted repeats (IRs, 29,765-29,934 bp). genomes contain 113 unique genes, including 79 protein coding 30 tRNA 4 rRNA genes. structures, gene contents, amino acid frequencies, codon usage patterns, RNA editing sites, simple sequence long conservative Zingiber. analysis divergence indicates following genes undergo positive selection (ccsA, ndhA, ndhB, petD, psbA, psbB, psbC, rbcL, rpl12, rpl20, rpl23, rpl33, rpoC2, rps7, rps12 ycf3). Eight highly variable regions identified seven intergenic (petA-pabJ, rbcL-accD, rpl32-trnL-UAG, rps16-trnQ-UUG, trnC-GCA-psbM, psbC-trnS-UGA ndhF-rpl32) one genic (ycf1). revealed sect. was sister to Cryptanthium rather than Pleuranthesis.This study reports 14 complete Overall, this provided solid backbone phylogeny polymorphisms we have uncovered sequencing offer rare possibility (for Zingiber) generation DNA markers. These results provide foundation future studies seek understand evolutionary dynamics or individual population variation

Language: Английский

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Plastome Evolution and Phylogeny of Orchidaceae, With 24 New Sequences

Frontiers in Plant Science, Journal Year: 2020, Volume and Issue: 11

Published: Feb. 21, 2020

In order to understand the evolution of orchid plastome, we annotated and compared 124 complete plastomes Orchidaceae representing all major lineages in their structures, gene contents, rearrangements IR contractions/expansions. Forty-two these were generated from corresponding author's laboratory, 24 plastomes—including nine genera (Amitostigma, Bulbophyllum, Dactylorhiza, Dipodium, Galearis, Gymnadenia, Hetaeria, Oreorchis, Sedirea)—are new this study. All plastomes, except Aphyllorchis montana, Epipogium aphyllum, Gastrodia elata, have a quadripartite structure consisting large single copy (LSC), two inverted repeats (IRs), small (SSC) region. The region was completely lost A. montana G. elata plastomes. SSC is E. aphyllum plastome. smallest plastome size 19,047 bp, roseum, largest 178,131 Cypripedium formosanum. sizes are primarily result losses associated with mycoheterotrophic habitats, while due expansion noncoding regions. minimal number common genes among maintain activity 15, including three subunits rpl (14, 16, 36), seven rps (2, 3, 4, 7, 8, 11, 14), rrn (5, 23), trnC-GCA, clpP genes. Three stages loss observed first ndh loss, which widespread Apostasioideae, Vanilloideae, Cypripedioideae, Epidendroideae, but rare Orchidoideae. second stage photosynthetic (atp, pet, psa, psb) rpo subunits, restricted Aphyllorchis, Hexalectris, some species Corallorhiza Neottia. third related prokaryotic expression (rpl, rps, trn, others), Epipogium, Gastrodia, Lecanorchis, Rhizanthella. addition, an intermediate between Cyrtosia (Vanilloideae). majority intron losses.

Language: Английский

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The chloroplast genome evolution of Venus slipper (Paphiopedilum): IR expansion, SSC contraction, and highly rearranged SSC regions

BMC Plant Biology, Journal Year: 2021, Volume and Issue: 21(1)

Published: May 31, 2021

Abstract Background Paphiopedilum is the largest genus of slipper orchids. Previous studies showed that phylogenetic relationships this are not well resolved, and sparse taxon sampling documented inverted repeat ( IR) expansion small single copy (SSC) contraction chloroplast genomes . Results Here, we sequenced, assembled, annotated 77 plastomes species (size range 152,130 – 164,092 bp). The phylogeny based on plastome resolved except for position two unstable species. We used comparative genomic approaches to elucidate evolution have a conserved genome structure gene content in SSC region. large copy/inverted (LSC/IR) boundaries relatively stable, while region (IR/SSC) varied among Corresponding IR/SSC boundary shifts, experienced IR contraction. incorporated one six genes Unexpectedly, great variation size, order, regions was found, especially subg. Parvisepalum Furthermore, provides evidence ongoing degradation ndh photoautotrophic plants. estimated substitution rates protein coding show accelerated clpP , psbH psbZ Genes transferred due shift also higher rates. Conclusions found with dense sampling, shows This an ideal system investigate dynamics evolution.

Language: Английский

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Phylogenomics and intergenomic conflict in a challenging orchid clade (Calypsoinae): monophyly of Corallorhiza, paraphyly of Oreorchis, and resurrection of Kitigorchis

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

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Relaxed selection underlies genome erosion in socially parasitic ant species

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: May 18, 2021

Inquiline ants are highly specialized and obligate social parasites that infiltrate exploit colonies of closely related species. They have evolved many times convergently, often evolutionarily young lineages, almost invariably rare. Focusing on the leaf-cutting ant genus Acromyrmex, we compared genomes three inquiline with their free-living, closely-related hosts. The parasite show distinct signatures erosion to host as a consequence relaxed selective constraints traits associated cooperative colony life inquilines having very small effective population sizes. We find parallel gene losses, particularly in olfactory receptors, consistent species reduced behavioral repertoires. Many genomic changes uncover resemble those observed non-social intracellular endosymbionts branched off into specialized, host-dependent niches.

Language: Английский

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A universal DNA barcode for the Tree of Life

Published: Jan. 18, 2024

Species identification using DNA barcodes has revolutionized biodiversity sciences and society at large. However, conventional barcoding methods do not reflect genomic complexity, may lack sufficient variation, rely on limited loci that are universal across the Tree of Life. Here, we develop a novel method uses exceptionally low-coverage genome skim data to create “varKode”, two-dimensional image representing landscape species. Using these varKodes, then train neural networks for precise taxonomic identification. Applying an expertly annotated dataset including hundreds newly sequenced samples from plant clade Malpighiales, demonstrate >91% precision when identifying species or genera. Remarkably, high accuracy remains despite minimal amounts lead failure applying alternative methods. We further illustrate broad utility varKodes several focal clades eukaryotes prokaryotes. As final test, classify entire NCBI eukaryote sequence-read archive identify its 861 constituent families with >95% utilizing less than 10 Mbp per sample. Enhanced computational efficiency scalability, inputs robust degraded DNA, modularity development make varKoding ideal approach science.

Language: Английский

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Unprecedented Parallel Photosynthetic Losses in a Heterotrophic Orchid Genus

Molecular Biology and Evolution, Journal Year: 2019, Volume and Issue: 36(9), P. 1884 - 1901

Published: April 25, 2019

Heterotrophic plants are evolutionary experiments in genomic, morphological, and physiological change. Yet, genomic sampling gaps exist among independently derived heterotrophic lineages, leaving unanswered questions about the process of genome modification. Here, we have sequenced complete plastid genomes for all species leafless orchid genus Hexalectris, including multiple individuals most, leafy relatives Basiphyllaea Bletia. Our objectives to determine number independent losses photosynthesis test hypotheses on degradation as a result relaxed selection. We demonstrate four five Hexalectris based photosynthetic apparatus, with but two displaying evidence losses, variation gene loss extending below level. Degradation atp complex is advanced warnockii, whereas only minimal (i.e., physical loss) has occurred some "housekeeping" genes. find rearrangements, shifts Inverted Repeat boundaries one accession H. arizonica, correlations substitutional attributes. unprecedented finding multiple, transitions fully mycoheterotrophic lifestyle single reveals that such land likely underestimated. This study underscores importance dense taxon sampling, which highly informative advancing models evolution heterotrophs. Mycoheterotrophs provide forward-genetic opportunities consequences radical beyond what possible mutational studies model organisms alone.

Language: Английский

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Evolution of plastid genomes of Holcoglossum (Orchidaceae) with recent radiation

BMC Evolutionary Biology, Journal Year: 2019, Volume and Issue: 19(1)

Published: Feb. 26, 2019

Abstract Background The plastid is a semiautonomous organelle with its own genome. Plastid genomes have been widely used as models for studying phylogeny, speciation and adaptive evolution. However, most studies focus on comparisons of genome evolution at high taxonomic levels, comparative the process plastome infrageneric or intraspecific level remain elusive. Holcoglossum small genus Orchidaceae, consisting approximately 20 species recent radiation . This made it an ideal group to explore mutation mode level. Results In this paper, we reported 15 complete from 12 1 Vanda. total length range between 145 kb 148 kb, encoding set 102 genes. whole ndh -gene families in truncated pseudogenized. Hairpin inversion coding region gene ycf2 has found. Conclusions Using comprehensive analysis, found that all indels different individuals same resulted copy number variation short repeat sequence, which may be caused by replication slippage. Annotation tandem repeats shows introduced widespread genomes. hairpin occurred randomly Orchidaceae.

Language: Английский

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Plastome Reduction in the Only Parasitic Gymnosperm Parasitaxus Is Due to Losses of Photosynthesis but Not Housekeeping Genes and Apparently Involves the Secondary Gain of a Large Inverted Repeat

Genome Biology and Evolution, Journal Year: 2019, Volume and Issue: 11(10), P. 2789 - 2796

Published: Aug. 21, 2019

Plastid genomes (plastomes) of parasitic plants undergo dramatic reductions as the need for photosynthesis relaxes. Here, we report plastome only known heterotrophic gymnosperm Parasitaxus usta (Podocarpaceae). With 68 unique genes, which 33 encode proteins, 31 tRNAs, and four rRNAs in a 85.3-kb length, has both smallest functionally least capable plastid genome gymnosperms. Although heterotroph retains chlorophyll, all genes are physically or lost, making photosynthetic energy gain impossible. The pseudogenization three plastome-encoded light-independent chlorophyll biosynthesis chlB, chlL, chlN implies that relies on either light-dependent pathway another regulation system. Nesting within group gymnosperms absence large inverted repeat regions (IRs), unusual feature is existence 9,256-bp long IR. Its short length gene composition completely differs from those IR-containing together suggest regain this critical, structure-stabilizing feature. In sum, our findings highlight particular path lifestyle-associated reductive evolution, where structural features might provide additional cues continued selection maintenance.

Language: Английский

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Comparative Plastome Analysis of Root- and Stem-Feeding Parasites of Santalales Untangle the Footprints of Feeding Mode and Lifestyle Transitions

Genome Biology and Evolution, Journal Year: 2019, Volume and Issue: 12(1), P. 3663 - 3676

Published: Dec. 13, 2019

Abstract In plants, parasitism triggers the reductive evolution of plastid genomes (plastomes). To disentangle molecular evolutionary associations between feeding on other plants below- or aboveground and general transitions from facultative to obligate parasitism, we analyzed 34 complete plastomes autotrophic, root- stem-feeding hemiparasitic, holoparasitic Santalales. We observed inexplicable losses housekeeping genes tRNAs in hemiparasites dramatic genomic reconfiguration Balanophoraceae, whose have exceptionally low GC contents. Genomic changes are related primarily hemi- holoparasitism, whereas transition a mode plays no major role. contrast, rate accelerates stepwise manner autotrophs then parasites. Already ancestral root-parasitism coincides with relaxation selection plastomes. Another significant selectional shift occurs as stem-feeders evolve, suggesting that this derived form trophic specialization despite retention photosynthetic capacity. Parasitic Santalales fill gap our understanding parasitism-associated plastome degeneration. reveal lifestyle-genome unfold interdependently over transitions, where Balanophoraceae provide system for exploring functional realms

Language: Английский

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