Genome Analysis of the Ancient Tracheophyte Selaginella tamariscina Reveals Evolutionary Features Relevant to the Acquisition of Desiccation Tolerance

Molecular Plant, Journal Year: 2018, Volume and Issue: 11(7), P. 983 - 994

Published: May 17, 2018

Resurrection plants, which are the "gifts" of natural evolution, ideal models for studying genetic basis plant desiccation tolerance. Here, we report a high-quality genome assembly 301 Mb diploid spike moss Selaginella tamariscina, primitive vascular resurrection plant. We predicated 27 761 protein-coding genes from assembled S. tamariscina genome, 11.38% (2363) showed significant expression changes in response to desiccation. Approximately 60.58% was annotated as repetitive DNA, is an almost 2-fold increase that desiccation-sensitive moellendorffii. Genomic and transcriptomic analyses highlight unique evolution complex regulations including species-specific expansion oleosin pentatricopeptide repeat gene families, pathways reactive oxygen species generation scavenging, enhanced abscisic acid (ABA) biosynthesis potentially distinct regulation ABA signaling response. Comparative analysis chloroplast genomes several revealed structural rearrangement complete loss NAD(P)H dehydrogenase (NDH) suggesting link between absence NDH Taken together, our comparative genomic reveal common tolerance strategies providing insights into mechanism plants.

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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Phylogenomics of Orchidaceae based on plastid and mitochondrial genomes

Molecular Phylogenetics and Evolution, Journal Year: 2019, Volume and Issue: 139, P. 106540 - 106540

Published: June 25, 2019

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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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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Apostasia Mitochondrial Genome Analysis and Monocot Mitochondria Phylogenomics

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(9), P. 7837 - 7837

Published: April 25, 2023

Apostasia shenzhenica belongs to the subfamily Apostasioideae and is a primitive group located at base of Orchidaceae phylogenetic tree. However, A. mitochondrial genome (mitogenome) still unexplored, relationships between monocots mitogenomes remain unexplored. In this study, we discussed genetic diversity within its monocotyledon mitogenome. We sequenced assembled complete mitogenome shenzhenica, resulting in circular draft 672,872 bp, with an average read coverage 122× GC content 44.4%. contained 36 protein-coding genes, 16 tRNAs, two rRNAs, copies nad4L. Repeat sequence analysis revealed large number medium small repeats, accounting for 1.28% sequence. Selection pressure indicated high conservation related species. RNA editing identified 416 sites region. Furthermore, found 44 chloroplast genomic DNA fragments that were transferred from five plastid-derived genes remaining intact Finally, 28 other showed evolution classification most well determined. These findings enrich resources orchids provide valuable information on taxonomic molecular monocots.

Language: Английский

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Complete Chloroplast Genomes of 9 Impatiens Species: Genome Structure, Comparative Analysis, and Phylogenetic Relationships

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(2), P. 536 - 536

Published: Jan. 10, 2025

Impatiens is a genus of functional herbaceous plants in the Balsaminaceae, which are not only great ornamental value and one world's top three flower bedding but also have wide range medicinal edible uses. Currently, taxonomy phylogenetic relationships species still controversial. In order to better understand their chloroplast properties evolution, nine (Impatiens repens, rectirostrata, baishaensis, rostellata, faberi, oxyanthera, tienchuanensis, blepharosepala, distracta) were sequenced, complete genomes analysed. Nine ranged length from 150,810 bp (I. rectirostrata) 152,345 blepharosepala). The all typical circular DNA molecules, GC content each region was consistent with published plants. results showed that seven mutational hotspots (trnL-UAG, ndhG, ycf1, ccsA, rrn23, trnA-UGC, ycf2) could be used as supporting data for further analyses tree identification. addition, support Balsaminaceae monophyletic taxon, Hydrocera triflora at base branch, original sister group relationship species. this paper enrich genomes, availability these will provide rich genetic information identification, thus enhancing taxonomic accuracy resolution Impatiens, promoting investigation rational use plant resources.

Language: Английский

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Gene losses and partial deletion of small single-copy regions of the chloroplast genomes of two hemiparasitic Taxillus species

Scientific Reports, Journal Year: 2017, Volume and Issue: 7(1)

Published: Oct. 4, 2017

Numerous variations are known to occur in the chloroplast genomes of parasitic plants. We determined complete genome sequences two hemiparasitic species, Taxillus chinensis and T. sutchuenensis, using Illumina PacBio sequencing technologies. These species first members family Loranthaceae be sequenced. The sutchuenensis comprise circular 121,363 122,562 bp-long molecules with quadripartite structures, respectively. Compared Nicotiana tabacum Osyris alba, all ndh genes as well three ribosomal protein genes, seven tRNA four ycf infA gene these have been lost. results maximum likelihood neighbor-joining phylogenetic trees strongly support theory that Viscaceae monophyletic clades. This research reveals effect a lifestyle on structure content enhances our understanding discrepancies terms assembly between PacBio.

Language: Английский

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Dense infraspecific sampling reveals rapid and independent trajectories of plastome degradation in a heterotrophic orchid complex

New Phytologist, Journal Year: 2018, Volume and Issue: 218(3), P. 1192 - 1204

Published: March 4, 2018

Summary Heterotrophic plants provide excellent opportunities to study the effects of altered selective regimes on genome evolution. Plastid (plastome) studies in heterotrophic are often based one or a few highly divergent species sequences as representatives an entire lineage, thus missing important evolutionary‐transitory events. Here, we present first infraspecific analysis plastome evolution any plant. By combining skimming and targeted sequence capture, address hypotheses degree rate degradation complex leafless orchids ( Corallorhiza striata ) across its geographic range. Plastomes strong support for relationships evidence reciprocal monophyly between C. involuta endangered bentleyi . Plastome is extensive, occurring rapidly over million years, with differing rates genomic change among two principal clades complex. Genome capture differ widely coverage depth overall, datasets varying immensely function GC content. These findings will help fill knowledge gap models plastid evolution, have implications future heterotrophs.

Language: Английский

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Plastid phylogenomic data yield new and robust insights into the phylogeny of Cleisostoma–Gastrochilus clades (Orchidaceae, Aeridinae)

Molecular Phylogenetics and Evolution, Journal Year: 2020, Volume and Issue: 145, P. 106729 - 106729

Published: Jan. 8, 2020

Language: Английский

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