Genome size variation and polyploidy prevalence in the genus Eragrostis are associated with the global dispersal in arid area

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: March 13, 2023

Biologists have long debated the drivers of genome size evolution and variation ever since Darwin. Assumptions for adaptive or maladaptive consequences associations between sizes environmental factors been proposed, but significance these hypotheses remains controversial. Eragrostis is a large genus in grass family often used as crop forage during dry seasons. The wide range complex ploidy levels make an excellent model investigating how associated with changes can ben interpreted.We reconstructed phylogeny estimated through flow cytometric analyses. Phylogenetic comparative analyses were performed to explore related their climatic niches geographical ranges. examined using different models study phylogenetic signal, mode tempo throughout evolutionary history.Our results support monophyly Eragrostis. ranged from ~0.66 pg ~3.80 pg. We found that moderate conservatism existed terms was absent factors. In addition, phylogeny-based revealed close correlations precipitation-related variables, indicating mainly caused by polyploidization may evolved adaptation various environments Eragrostis.This first take global perspective on Our suggest are manifested variation, allowing arid species spread xeric area world.

Language: Английский

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Comparative analyses and phylogenetic relationships of thirteen Pholidota species (Orchidaceae) inferred from complete chloroplast genomes

BMC Plant Biology, Journal Year: 2023, Volume and Issue: 23(1)

Published: May 20, 2023

Abstract Background The orchid genus Pholidota Lindl. ex Hook. is economically important as some species has long been used in traditional medicine. However, the systematic status of and intergeneric relationships inferred from previous molecular studies are unclear due to insufficient sampling lack informative sites. So far, only limited genomic information available. taxonomy remains unresolved somewhat controversial. In this study, complete chloroplast (cp.) genomes thirteen were sequenced analyzed gain insight into phylogeny mutation patterns their cp. genomes. Results All examined exhibited typical quadripartite circular structures, with size ranging 158,786 159,781 bp. annotation contained a total 135 genes each genome, i.e., 89 protein-coding genes, 38 tRNA eight rRNA genes. codon usage analysis indicated preference A/U-ending codons. Repeat sequence identified 444 tandem repeats, 322 palindromic repeats 189 dispersed repeats. A 525 SSRs, 13,834 SNPs 8,630 InDels detected. Six mutational hotspots potential markers. These markers highly variable regions expected facilitate future genetic studies. Our phylogenetic analyses confirmed polyphyletic , grouped four main clades: s.s. was resolved sister clade containing Coelogyne ; other two clades clustered together Bulleyia Panisea respectively; P. ventricosa placed at basal position, deviated all species. Conclusion This first study comprehensively examine variations systematically analyze evolution based on plastid data. findings contribute better understanding genome provide new insights its closely related genera within subtribe Coelogyninae. research laid foundation for evolutionary mechanisms classification medicinally genus.

Language: Английский

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Persistent Habitat Instability and Patchiness, Sexual Attraction, Founder Events, Drift and Selection: A Recipe for Rapid Diversification of Orchids

Plants, Journal Year: 2025, Volume and Issue: 14(8), P. 1193 - 1193

Published: April 11, 2025

Orchidaceae is one of the most species-rich families flowering plants, with current diversity having evolved within last 5 My. Patterns associated species richness and rapid diversification have been identified but not often evolutionary processes. We review frequently correlates suggest that processes rate by which they occur vary geographically are largely dependent on persistent pulses habitat instabilities, especially for epiphytes. Aggressive orogenesis creates fragmented habitats while global climatic cycles exacerbate ecological instabilities. The need repeated dispersal results in frequent founder events, sets stage allopatric via bouts genetic drift natural selection. allopatry requirement can be bypassed pollination systems involving flowers attracting pollinators through production sex signaling semiochemicals. drift-selection model diversification, coupled instability throughout geological time scales, likely components a multifactorial process leading to rapid, recent this family.

Language: Английский

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Decoding the mitogenome of rosemary (Salvia rosmarinus): insights into genome evolution, structural dynamics and prospects for mitochondrial engineering

BMC Plant Biology, Journal Year: 2025, Volume and Issue: 25(1)

Published: April 17, 2025

Rosemary (Salvia rosmarinus), an aromatic evergreen shrub of the Salvia (Lamiaceae), is native to Mediterranean region, thriving in rocky or arid soils. Widely used food, pharmaceuticals, and cosmetics, its clonal reproduction poses significant challenges for breeding germplasm innovation. While mitogenome engineering holds promise introducing heritable mutations, incomplete information rosemary has hindered such efforts. This study addresses this gap by assembling analyzing complete S. rosmarinus, focusing on structure, repetitive sequences, RNA editing events, intracellular gene transfer (IGT), phylogenetic relationships. The rosmarinus spans 384,113 bp with a GC content 44.8%, containing 34 unique protein-coding genes 114 simple sequence repeats. Comparative analysis revealed 28 homologous segments shared between plastome, totaling 18,675 length. Furthermore, fragments nuclear organellar genomes were identified, including 1,069,255 organelle-derived sequences genome, 194,689 from plastid DNA transfers (NUPTs) 15,192 mitochondrial (NUMTs). NUPTs more abundant contributed significantly total Synteny eight Lamiales species extensive mitogenomic recombination structural rearrangements. These findings highlight dynamic nature mitogenomes, offering insights into genome evolution supporting future programs enhance genetic diversity adaptability rosmarinus. provides first revealing dispersed repeats, editing, horizontal organelle genomes. exhibits typical circular structure evidence frequent recombination, providing valuable genetics, evolution, molecular biology.

Language: Английский

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Repeat proliferation and partial endoreplication jointly shape the patterns of genome size evolution in orchids

The Plant Journal, Journal Year: 2021, Volume and Issue: 107(2), P. 511 - 524

Published: May 8, 2021

Summary Although the evolutionary drivers of genome size change are known, general patterns and mechanisms plant evolution yet to be established. Here we aim assess relative importance proliferation repetitive DNA, chromosomal variation (including polyploidy), type endoreplication for Pleurothallidinae, most species‐rich orchid lineage. Phylogenetic relationships between 341 Pleurothallidinae representatives were refined using a target enrichment hybrid capture combined with high‐throughput sequencing approach. Genome assessed flow cytometry supplemented karyological analysis low‐coverage Illumina repeatome on subset samples. Data analyzed phylogeny‐based models. diversity (0.2–5.1 Gbp) was mostly independent profound chromosome count (2 n = 12–90) but tightly linked overall content DNA elements. Species partial (PE) had significantly greater sizes, genomic repeat correlated non‐endoreplicated part genome. In PE species, is preferentially accumulated in parts their genomes. Our results demonstrate that elements together shape orchids.

Language: Английский

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Repeat-based phylogenomics shed light on unclear relationships in the monocentric genus Juncus L. (Juncaceae)

Molecular Phylogenetics and Evolution, Journal Year: 2023, Volume and Issue: 189, P. 107930 - 107930

Published: Sept. 16, 2023

Language: Английский

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A cytosystematic study of the Dianthus virgineus complex (Caryophyllaceae) in the Central Mediterranean

Journal of Systematics and Evolution, Journal Year: 2023, Volume and Issue: 62(4), P. 589 - 602

Published: Oct. 23, 2023

Abstract European wild carnations ( Dianthus ) are represented by a high number of taxa organized in unresolved taxonomies. In particular, belonging to the virgineus L. complex Central Mediterranean have been delimited mainly with qualitative morphological data and still await quantitative investigations, which vital understand boundaries relations among plant diversity groups. Here, we examine phenotypic features nuclear genome organization testing for species this complex. We studied chromosome number, total haploid length (THL), relative size (RGS) 122 populations 25 out 33 All 2 n = x 30 chromosomes, THL ranges from 14.09 20.71 μm. Genome estimations support absence polyploidization events, but show certain degree variation (0.318–0.423 arbitrary units). The RGS is not agreement current taxonomic treatment, rather shows geographical pattern, higher values Sicily Sardinia. No correlation between was detected, possibly due stable small chromosomes. A evolutionary unique groups lower than currently accepted may be hypothesized.

Language: Английский

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The specific DNA barcodes based on chloroplast genes for species identification of Theaceae plants

Physiology and Molecular Biology of Plants, Journal Year: 2022, Volume and Issue: 28(4), P. 837 - 848

Published: April 1, 2022

Language: Английский

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In-depth analysis of genomes and functional genomics of orchid using cutting-edge high-throughput sequencing

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: Sept. 23, 2022

High-throughput sequencing technology has been facilitated the development of new methodologies and approaches for studying origin evolution plant genomes subgenomes, population domestication, functional genomics. Orchids have tens thousands members in nature. Many them promising application potential extension conservation ecological chain, horticultural use ornamental blossoms, utilization botanical medicines. However, a large-scale gene knockout mutant library sophisticated genetic transformation system are still lacking improvement orchid germplasm resources. New editing tools, such as favored CRISPR-Cas9 or some base editors, not yet widely applied orchids. In addition to large variety cultivars, high-precision, high-throughput genome is also required mining trait-related genes. Nowadays, focus genomics research directed classification species, deletion, duplication chromosomal polyploidy, flower morphogenesis-related regulation. Here, progressing achieved molecular biology over past few decades discussed, including size polyploidization. The frequent incorporation LTR retrotransposons play important role expansion structural variation genome. event nuclear generated plenty recently tandem duplicated genes, which drove divergency loss plastid genome, mostly affected genes related photosynthesis autotrophy, demonstrated that orchids experienced more separate transitions heterotrophy than any other terrestrial plant. Moreover, resequencing provide useful SNP markers constructing maps, will facilitate breeding novel varieties. significance technologies identification provides us with representative trait-improving well mechanisms worthy further investigation. addition, promise investigation function. This knowledge may scientific reference theoretical basis studies.

Language: Английский

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Complete mitogenome assembly of Selenicereus monacanthus revealed its molecular features, genome evolution, and phylogenetic implications

BMC Plant Biology, Journal Year: 2023, Volume and Issue: 23(1)

Published: Nov. 4, 2023

Mitochondria are the powerhouse of cell and critical for plant growth development. Pitaya (Selenicereus or Hylocereus) is most important economic crop in family Cactaceae grown worldwide, however its mitogenome unreported.This study assembled complete red skin flesh pitaya monacanthus). It a full-length, 2,290,019 bp circular molecule encoding 59 unique genes that only occupy 2.17% entire length. In addition, 4,459 pairs dispersed repeats (≥ 50 bp) were identified, accounting 84.78% total length, three (394,588, 124,827, 13,437 mediating genomic recombination identified by long read mapping Sanger sequencing. RNA editing events all 32 protein-coding (PCGs), among which four sites (nad1-2, nad4L-2, atp9-copy3-223, ccmFC-1309) associated with initiation termination PCGs. Seventy-eight homologous fragments chloroplast genome mitogenome, longest having 4,523 bp. evolutionary analyses suggest S. monacanthus may have undergone multiple reorganization during evolution, loss at least nine PCGs (rpl2, rpl10, rps2, rps3, rps10, rps11, rps14, rps19, sdh3).This revealed genetic basis provided scientific further research on phenotypic traits germplasm resource

Language: Английский

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