CAM evolution is associated with gene family expansion in an explosive bromeliad radiation DOI Creative Commons
Clara Groot Crego, Jaqueline Hess, Gil Yardeni

и другие.

The Plant Cell, Год журнала: 2024, Номер 36(10), С. 4109 - 4131

Опубликована: Апрель 30, 2024

The subgenus Tillandsia (Bromeliaceae) belongs to one of the fastest radiating clades in plant kingdom and is characterized by repeated evolution Crassulacean acid metabolism (CAM). Despite its complex genetic basis, this water-conserving trait has evolved independently across many families regarded as a key innovation driver ecological diversification Bromeliaceae. By producing high-quality genome assemblies species pair displaying divergent photosynthetic phenotypes, combining genome-wide investigations synteny, transposable element (TE) dynamics, sequence evolution, gene family temporal differential expression, we were able pinpoint genomic drivers CAM Tillandsia. Several large-scale rearrangements associated with karyotype changes between 2 genomes highly dynamic TE landscape shaped However, our analyses show that rewiring mainly obtained through regulatory rather than coding CAM-related genes are differentially expressed 24-h cycle but not candidates positive selection. Gene orthology reveal manifesting expression underwent accelerated expansion constitutive species, further supporting view evolution.

Язык: Английский

NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes DOI Creative Commons
Weiming He, Jian Yang, Jing Yi

и другие.

Bioinformatics, Год журнала: 2023, Номер 39(3)

Опубликована: Март 1, 2023

Abstract Summary Large-scale comparative genomic studies have provided important insights into species evolution and diversity, but also lead to a great challenge visualize. Quick catching or presenting key information hidden in the vast amount of data relationships among multiple genomes requires an efficient visualization tool. However, current tools for such remain inflexible layout and/or require advanced computation skills, especially genome-based synteny. Here, we developed easy-to-use flexible tool, NGenomeSyn [multiple (N) Genome Synteny], publication-ready syntenic whole genome local region features (e.g. repeats, structural variations, genes) across with high customization. provides easy way its users visualize large rich by simply adjusting options moving, scaling, rotation target genomes. Moreover, could be applied on non-genomic similar input formats. Availability implementation is freely available at GitHub (https://github.com/hewm2008/NGenomeSyn) Zenodo (https://doi.org/10.5281/zenodo.7645148).

Язык: Английский

Процитировано

84
Newly identified sex chromosomes in the Sphagnum (peat moss) genome alter carbon sequestration and ecosystem dynamics DOI Creative Commons
Adam Healey, Bryan Piatkowski, John T. Lovell

и другие.

Nature Plants, Год журнала: 2023, Номер 9(2), С. 238 - 254

Опубликована: Фев. 6, 2023

Peatlands are crucial sinks for atmospheric carbon but critically threatened due to warming climates. Sphagnum (peat moss) species keystone members of peatland communities where they actively engineer hyperacidic conditions, which improves their competitive advantage and accelerates ecosystem-level sequestration. To dissect the molecular physiological sources this unique biology, we generated chromosome-scale genomes two species: S. divinum angustifolium. show no gene colinearity with any other reference genome date, demonstrating that represents an unsampled lineage land plant evolution. The also revealed average recombination rate order magnitude higher than vascular plants short putative U/V sex chromosomes. These newly described chromosomes interact autosomal loci significantly impact growth across diverse pH conditions. This discovery demonstrates ability sequester in acidic peat bogs is mediated by interactions between sex, autosomes environment.

Язык: Английский

Процитировано

48
The complex polyploid genome architecture of sugarcane DOI Creative Commons
Adam Healey, Olivier Garsmeur, John T. Lovell

и другие.

Nature, Год журнала: 2024, Номер 628(8009), С. 804 - 810

Опубликована: Март 27, 2024

Sugarcane, the world's most harvested crop by tonnage, has shaped global history, trade and geopolitics, is currently responsible for 80% of sugar production worldwide

Язык: Английский

Процитировано

48
Pan-phylum genomes of hornworts reveal conserved autosomes but dynamic accessory and sex chromosomes DOI
Peter Schafran,

Duncan A. Hauser,

Jessica Nelson

и другие.

Nature Plants, Год журнала: 2025, Номер unknown

Опубликована: Янв. 3, 2025

Язык: Английский

Процитировано

5
Leveraging a phased pangenome for haplotype design of hybrid potato DOI Creative Commons
Lin Cheng, Nan Wang, Zhigui Bao

и другие.

Nature, Год журнала: 2025, Номер unknown

Опубликована: Янв. 22, 2025

Язык: Английский

Процитировано

5
Photosymbiosis shaped animal genome architecture and gene evolution as revealed in giant clams DOI Creative Commons
Ruiqi Li, Carlos Leiva, Sarah Lemer

и другие.

Communications Biology, Год журнала: 2025, Номер 8(1)

Опубликована: Янв. 4, 2025

Abstract Symbioses are major drivers of organismal diversification and phenotypic innovation. However, how long-term symbioses shape whole genome evolution in metazoans is still underexplored. Here, we use a giant clam ( Tridacna maxima ) to demonstrate symbiosis has left complex signatures an animal’s genome. Giant clams thrive oligotrophic waters by forming remarkable association with photosymbiotic dinoflagellate algae. Genome-based demographic inferences uncover tight correlation between T. global population change paleoclimate habitat shifts, revealing abiotic biotic factors may dictate microevolution. Comparative analyses reveal genomic features that be symbiosis-driven, including expansion contraction immunity-related gene families large proportion lineage-specific genes. Strikingly, about 70% the composed repetitive elements, especially transposable most likely resulting from symbiosis-adapted immune system. This work greatly enhances our understanding underlie metazoan diversification.

Язык: Английский

Процитировано

3
Duckweed genomes and epigenomes underlie triploid hybridization and clonal reproduction DOI Creative Commons
Evan Ernst, Bradley W. Abramson, Kenneth Acosta

и другие.

Current Biology, Год журнала: 2025, Номер unknown

Опубликована: Апрель 1, 2025

The Lemnaceae (duckweeds) are the world's smallest but fastest-growing flowering plants. Prolific clonal propagation facilitates continuous micro-cropping for plant-based protein and starch production holds tremendous promise sequestration of atmospheric CO2. Here, we present chromosomal assemblies, annotations, phylogenomic analysis Lemna genomes that uncover candidate genes responsible unique metabolic developmental traits family, such as anatomical reduction, adaxial stomata, lack stomatal closure, carbon via crystalline calcium oxalate. have selectively lost required RNA interference, including Argonaute reproductive isolation (the triploid block) haploid gamete formation. Triploid hybrids arise commonly among Lemna, found mutations in highly conserved meiotic crossover could support polyploid meiosis. Further, mapping centromeres by chromatin immunoprecipitation suggests their epigenetic origin despite divergence underlying tandem repeats centromeric retrotransposons. Syntenic comparisons with Wolffia Spirodela reveal diversification these genera coincided "Azolla event" mid-Eocene, during which aquatic macrophytes reduced high CO2 levels to those current ice age. Facile regeneration transgenic fronds from tissue culture, aided silencing, makes a powerful biotechnological platform, exemplified recent engineering high-oil outperforms oil-seed crops.

Язык: Английский

Процитировано

3
Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet DOI Creative Commons
Katrien M. Devos, Peng Qi, Bochra A. Bahri

и другие.

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Июнь 21, 2023

Abstract Finger millet is a key food security crop widely grown in eastern Africa, India and Nepal. Long considered ‘poor man’s crop’, finger has regained attention over the past decade for its climate resilience nutritional qualities of grain. To bring breeding into 21 st century, here we present assembly annotation chromosome-scale reference genome. We show that this ~1.3 million years old allotetraploid high level homoeologous gene retention lacks subgenome dominance. Population structure mainly driven by differential presence large wild segments pericentromeric regions several chromosomes. Trait mapping, followed variant analysis candidates, reveals loss purple coloration anthers stigma associated with loss-of-function mutations orthologs maize R1 / B1 Arabidopsis GL3/EGL3 anthocyanin regulatory genes. Proanthocyanidin production seed not affected these knockouts.

Язык: Английский

Процитировано

39
Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea DOI
Aamir W. Khan, Vanika Garg, Shuai Sun

и другие.

Nature Genetics, Год журнала: 2024, Номер 56(6), С. 1225 - 1234

Опубликована: Май 23, 2024

Язык: Английский

Процитировано

17
Phased Assembly of Neo-Sex Chromosomes Reveals Extensive Y Degeneration and Rapid Genome Evolution in Rumex hastatulus DOI Creative Commons
Bianca M. Sacchi, Zoë Humphries,

Jana Kružlicová

и другие.

Molecular Biology and Evolution, Год журнала: 2024, Номер 41(4)

Опубликована: Апрель 1, 2024

Abstract Y chromosomes are thought to undergo progressive degeneration due stepwise loss of recombination and subsequent reduction in selection efficiency. However, the timescales evolutionary forces driving remain unclear. To investigate evolution sex on multiple timescales, we generated a high-quality phased genome assembly massive older (<10 MYA) neo (<200,000 yr) XYY cytotype dioecious plant Rumex hastatulus hermaphroditic outgroup salicifolius. Our assemblies, supported by fluorescence situ hybridization, confirmed that neo-sex were formed two key events: an X-autosome fusion reciprocal translocation between homologous autosome chromosome. The enormous sex-linked regions X (296 Mb) (503 both evolved from large repeat-rich genomic with low recombination; however, complete still led over 30% gene major rearrangements. In region, there has been significant increase transposable element abundance, even into near genes. neo-sex-linked regions, observed evidence extensive rearrangements without loss. Overall, inferred during first 10 million years chromosome but not very short timescales. results indicate when emerge repetitive already-low recombination, leads substantial content degeneration.

Язык: Английский

Процитировано

13