Methods in molecular biology, Год журнала: 2023, Номер unknown, С. 211 - 225
Опубликована: Янв. 1, 2023
Язык: Английский
Journal of Systematics and Evolution, Год журнала: 2021, Номер 59(4), С. 852 - 895
Опубликована: Май 9, 2021
Abstract Cyperaceae (sedges) are the third largest monocot family and of considerable economic ecological importance. Sedges represent an ideal model to study evolutionary biology due their species richness, global distribution, large discrepancies in lineage diversity, broad range preferences, adaptations including multiple origins C 4 photosynthesis holocentric chromosomes. Goetghebeur′s seminal work on published 1998 provided most recent complete classification at tribal generic level, based a morphological inflorescence, spikelet, flower, embryo characters, plus anatomical other information. Since then, several family‐level molecular phylogenetic studies using Sanger sequence data have been published. Here, more than 20 years after last comprehensive family, we present first family‐wide phylogenomic targeted sequencing Angiosperms353 probe kit sampling 311 accessions. In addition, 62 accessions available from GenBank were mined for overlapping reads included analyses. Informed by this backbone phylogeny, new tribal, subtribal, levels is proposed. The majority previously recognized suprageneric groups supported, time, establish support tribe Cryptangieae as clade genus Koyamaea . We provide taxonomic treatment identification keys diagnoses 2 subfamilies, 24 tribes, 10 subtribes, basic information 95 genera. includes five subtribes Schoeneae: Anthelepidinae, Caustiinae, Gymnoschoeninae, Lepidospermatinae, Oreobolinae.
Язык: Английский
Процитировано
84
Molecular Biology and Evolution, Год журнала: 2023, Номер 40(3)
Опубликована: Фев. 22, 2023
Abstract Chromosome rearrangements are thought to promote reproductive isolation between incipient species. However, it is unclear how often, and under what conditions, fission fusion act as barriers gene flow. Here we investigate speciation two largely sympatric fritillary butterflies, Brenthis daphne ino. We use a composite likelihood approach infer the demographic history of these species from whole-genome sequence data. then compare chromosome-level genome assemblies individuals each identify total nine chromosome fissions fusions. Finally, fit model where effective population sizes migration rate vary across genome, allowing us quantify effects on isolation. show that chromosomes involved in experienced less since onset divergence genomic regions near rearrangement points have further reduction rate. Our results suggest evolution multiple B. ino populations, including alternative fusions same chromosomes, resulted Although unlikely be only processes led this study shows can directly may when karyotypes evolve quickly.
Язык: Английский
Процитировано
38
Cold Spring Harbor Perspectives in Biology, Год журнала: 2023, Номер 15(11), С. a041447 - a041447
Опубликована: Авг. 21, 2023
Kay Lucek1, Mabel D. Giménez2,3, Mathieu Joron4, Marina Rafajlović5,6, Jeremy B. Searle7, Nora Walden8, Anja Marie Westram9,10 and Rui Faria11,12 1Biodiversity Genomics Laboratory, Institute of Biology, University Neuchâtel, 2000 Switzerland 2Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Genética Humana Misiones (IGeHM), Parque la Salud Provincia "Dr. Ramón Madariaga," N3300KAZ Posadas, Misiones, Argentina 3Facultad Ciencias Exactas Químicas Naturales, Universidad N3300LQH 4Centre d'Ecologie Fonctionnelle et Evolutive, Université Montpellier, CNRS, EPHE, IRD, 34293 France 5Department Marine Sciences, Gothenburg, 405 30 Sweden 6Centre for Evolutionary 7Department Ecology Cornell University, Ithaca, New York 14853, USA 8Centre Organismal Studies, Heidelberg, 69117 Germany 9Institute Science Technology Austria (ISTA), 3400 Klosterneuburg, 10Faculty Biosciences Aquaculture, Nord 8026 Bodø, Norway 11CIBIO, Centro Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, CIBIO, Campus Vairão, Universidade do Porto, 4485-661 Portugal 12BIOPOLIS Program in Genomics, Biodiversity Land Planning, Correspondence: kay.lucek{at}unine.ch; ruifaria{at}cibio.up.pt
Язык: Английский
Процитировано
26
Trends in Ecology & Evolution, Год журнала: 2022, Номер 37(8), С. 655 - 662
Опубликована: Апрель 26, 2022
Язык: Английский
Процитировано
34
Molecular Ecology, Год журнала: 2023, Номер 33(24)
Опубликована: Июль 24, 2023
Holocentric organisms, unlike typical monocentric have kinetochore activity distributed along almost the whole length of chromosome. Because this, chromosome rearrangements through fission and fusion are more likely to become fixed in holocentric species, which may account for extraordinary rates evolution that many lineages exhibit. Long blocks genome synteny been reported animals with chromosomes despite high rearrangements. Nothing is known from plants, however, fact holocentricity appears played a key role diversification one largest angiosperm genera, Carex (Cyperaceae). In current study, we compared genomes species distantly related Cyperaceae characterize conserved rearranged regions. Our analyses span divergence times ranging between 2 50 million years. We also C. scoparia chromosome-level assembly linkage map same study at population level suppression recombination patterns. found longer than expected under null model random rearrangement breakpoints, even very species. repetitive DNA be non-randomly associated holocentromeres regions genome. The evidence sedges suggests genomic hotspots shape recombination, gene order crossability sedges. This finding help explain why able maintain cohesion face interspecific
Язык: Английский
Процитировано
15
Annals of Botany, Год журнала: 2022, Номер 130(7), С. 999 - 1014
Опубликована: Ноя. 7, 2022
Abstract Background and Aims While variation in genome size chromosome numbers their consequences are often investigated plants, the biological relevance of remains poorly known. Here, we examine mean cyperid clade (families Cyperaceae, Juncaceae Thurniaceae), which is largest vascular plant lineage with predominantly holocentric chromosomes. Methods We measured 436 species cyperids using flow cytometry, augment these data previously published datasets. then separately compared sizes (2C/2n) amongst major lineages analysed how two genomic traits associated various environmental factors phylogenetically informed methods. Key Results show that have smallest recorded seed a large divergence between values. found smaller chromosomes larger geographical distributions there strong inverse association number across this lineage. Conclusions The distinct patterns might be explained by holokinetic drive. numerous small function to increase genetic diversity where crossovers limited during meiosis.
Язык: Английский
Процитировано
21
BMC Plant Biology, Год журнала: 2024, Номер 24(1)
Опубликована: Июль 3, 2024
Abstract Background Cyperus stoloniferus is an important species in coastal ecosystems and possesses economic ecological value. To elucidate the structural characteristics, variation, evolution of organelle genome C. , we sequenced, assembled, compared its mitochondrial chloroplast genomes. Results We assembled genomes . The total length (mtDNA) was 927,413 bp, with a GC content 40.59%. It consists two circular DNAs, including 37 protein-coding genes (PCGs), 22 tRNAs, five rRNAs. (cpDNA) 186,204 containing 93 PCGs, 40 8 mtDNA cpDNA contained 81 129 tandem repeats, respectively, 346 1,170 dispersed both which have 270 simple sequence repeats. third high-frequency codon (RSCU > 1) organellar tended to end at A or U, whereas low-frequency < G RNA editing sites PCGs were relatively few, only 9 23 cpDNA, respectively. 28 plastid DNAs (MTPTs) derived from three complete trnT-GGU trnH-GUG trnS-GCU Phylogeny collinearity indicated that relationship between rotundus are closest. rns gene exhibited greatest nucleotide variability, variability infA Most negatively selected highly evolutionarily conserved. Only six Ka/Ks 1; particular, atp9 atp6 rps7 may undergone potential positive selection. Conclusion validated contains 15,034 bp reverse complementary sequence. provides valuable genomic resources for identification, evolution, comparative research Cyperaceae.
Язык: Английский
Процитировано
5
Molecular Ecology, Год журнала: 2023, Номер 33(24)
Опубликована: Авг. 14, 2023
Repetitive elements can cause large-scale chromosomal rearrangements, for example through ectopic recombination, potentially promoting reproductive isolation and speciation. Species with holocentric chromosomes, that lack a localized centromere, might be more likely to retain rearrangements lead karyotype changes such as fusions fissions. This is because chromosome segregation during cell division should less affected than in organisms centromere. The relationships between repetitive how they may translate patterns of speciation are though poorly understood. Here, we use reference-free approach based on low-coverage short-read sequencing data characterize the repeat landscape two independently evolved groups: Erebia butterflies Carex sedges. We consider both micro- macro-evolutionary scales investigate differentiation populations association repeats phylogenetic framework Carex. At micro-evolutionary scale, found population increases overall intraspecific genetic among four species. indications an along phylogenies. Altogether, our results suggest associated level clades therefore play role adaptation species diversification.
Язык: Английский
Процитировано
11
Plant Cell & Environment, Год журнала: 2025, Номер unknown
Опубликована: Май 27, 2025
ABSTRACT Eukaryotic centromeres highlight the remarkable plasticity of eukaryotic chromosomes through their conserved functionality and sequence divergence. Holocentric chromosomes, where centromere activity is distributed along entire chromosome length, offer a unique model for investigating molecular mechanisms underlying adaptive evolution between chromosomes. In this review, we summarise speculate on multiple changes prerequisites potentially involved in holocentromeres. The interplay environmental factors, chromosomal rearrangements, drives transition from regional to holocentric characteristics. centromeric histone H3 (CenH3) protein mediates neocentromere formation by recognising non‐centromeric regions with appropriate AT content, thereby facilitating restructuring Dynamic repetitive sequences provide functional sites assembly, recombination repair spreading maturation. Epigenetic modifications maintain coordination among units modulating chromatin states, CenH3 localisation, kinetochore assembly. This review provides comprehensive framework understanding evolutionary holocentromeres derived monocentromere offers insights into design artificial centromeres.
Язык: Английский
Процитировано
0
DNA Research, Год журнала: 2022, Номер 30(1)
Опубликована: Дек. 12, 2022
Abstract Kobresia species are common in meadows on the Qinghai–Tibet Plateau. They important food resources for local livestock, and serve a critical foundation ecosystem integration. Genetic of scarce. Here, we generated chromosome-level genome assembly K. myosuroides (Cyperaceae), using PacBio long-reads, Illumina short-reads, Hi–C technology. The final had total size 399.9 Mb with contig N50 value 11.9 Mb. result supported 29 pseudomolecules model which was consistent cytological results. A 185.5 (44.89% genome) transposable elements were detected, 26,748 protein-coding genes predicted. Comparative analysis revealed that plants have experienced recent diversification events during late Miocene to Pliocene. Karyotypes indicated fission fusion chromosomes been major driver speciation, complied lack whole-genome duplication (WGD) genome. Generally, this high-quality reference provides insights into evolution alpine sedges, may be helpful endemic forage improvement preservation.
Язык: Английский
Процитировано
11