Dynamic evolution of a sex-linked region DOI Creative Commons
Xiaomeng Mao, Nima Rafati, Christian Tellgren‐Roth

et al.

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 10, 2025

Abstract Background Sex chromosomes often evolve exceptionally fast and degenerate after recombination arrest. However, the underlying evolutionary processes are under persistent debate, particularly whether or not arrest evolves in a stepwise manner how switches sex determination genes contribute to chromosome evolution. Here, we study dioecious plant genus Salix with high turnover of chromosomes. Results We identified Z W sex-linked regions (~ 8 Mb) on 15 dwarf willow Salix herbacea using new haplotype-resolved assembly. The region harboured large (5 embedded inversion. Analyses synteny other species, sequence divergence between degeneration suggest that inversion recently incorporated pseudoautosomal sequences into region, extending its length nearly three-fold. W-hemizygous exclusively contained seven pairs inverted partial repeats male essential floral identity gene PISTILLATA, suggesting possible PISTILLATA suppression mechanism by interfering RNA females. Such pseudogenes were also found species ZW but those XY determination. Conclusions Our provides rare compelling direct support for long-standing theory reduction mediated inversions suggests Salicaceae family is associated switch gene.

Language: Английский

Genome assembly in the telomere-to-telomere era DOI
Heng Li, Richard Durbin

Nature Reviews Genetics, Journal Year: 2024, Volume and Issue: 25(9), P. 658 - 670

Published: April 22, 2024

Language: Английский

Citations

65
A pangenome reveals LTR repeat dynamics as a major driver of genome evolution in Chenopodium DOI Creative Commons

Kate E. Jaggi,

Karol Krak, Helena Štorchová

et al.

The Plant Genome, Journal Year: 2025, Volume and Issue: 18(1)

Published: Feb. 28, 2025

Abstract The genus Chenopodium L. is characterized by its wide geographic distribution and ecological adaptability. Species such as quinoa ( Willd.) have served domesticated staple crops for centuries. Wild species exhibit diverse niche adaptations are important genetic reservoirs beneficial agronomic traits, including disease resistance climate hardiness. To harness the potential of wild taxa crop improvement, we developed a pangenome through assembly comparative analyses 12 that encompass eight known genome types (A–H). Six new chromosome‐scale assemblies, many polyploids; thus, total 20 genomes were included in analyses. We show vary dramatically size with D being smallest (∼370 Mb) B largest (∼700 was correlated independent expansions Copia Gypsy LTR retrotransposon families, suggesting transposable elements played critical role evolution genomes. annotated 33,457 pan‐ gene which ∼65% classified shell (2% private). Phylogenetic analysis clarified evolutionary relationships among lineages, notably resolving taxonomic placement F while highlighting uniqueness A Western Hemisphere. These genomic resources particularly understanding secondary tertiary pools available improvement chenopods furthering our complexity within genus.

Language: Английский

Citations

2
A new gene finding tool GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes DOI Creative Commons
Tomáš Brůna,

Alexandre Lomsadze,

Mark Borodovsky

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Jan. 15, 2023

Large-scale genomic initiatives, such as the Earth BioGenome Project, require efficient methods for eukaryotic genome annotation. Here we present an automatic gene finder, GeneMark-ETP, integrating genomic-, transcriptomic- and protein-derived evidence that has been developed with a focus on large plant animal genomes. GeneMark-ETP first identifies loci where extrinsic data is sufficient making predictions 'high confidence'. The genes situated in space between high confidence are predicted next stage. set of serves initial training statistical model. Further on, model parameters iteratively updated rounds prediction parameter re-estimation. Upon reaching convergence, makes final delivers whole complement genes. outperformed finders using single type evidence. Comparisons utilizing both transcript- evidence, MAKER2, TSEBRA, demonstrated delivered state-of-the-art accuracy margin outperforming existing approaches increasing its applications to larger more complex

Language: Английский

Citations

32
The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics DOI Creative Commons
Ann M. Mc Cartney, Giulio Formenti, Alice Mouton

et al.

npj Biodiversity, Journal Year: 2024, Volume and Issue: 3(1)

Published: Sept. 17, 2024

A genomic database of all Earth's eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction have information available. In 2018, scientists across the world united under Earth BioGenome Project (EBP), aiming produce high-quality reference genomes containing ~1.5 million recognized species. As European node EBP, Reference Genome Atlas (ERGA) sought implement new decentralised, equitable and inclusive model for producing genomes. For this, ERGA launched Pilot establishing first distributed genome production infrastructure testing it on 98 from 33 countries. Here we outline explore its effectiveness scaling production, whilst considering equity inclusion. The outcomes lessons learned provide solid foundation while offering key learnings other transnational, national resource projects EBP.

Language: Английский

Citations

12
Haplotype-resolved genome assembly provides insights into evolutionary history of the Actinidia arguta tetraploid DOI Creative Commons
Feng Zhang, Yingzhen Wang, Yunzhi Lin

et al.

Molecular Horticulture, Journal Year: 2024, Volume and Issue: 4(1)

Published: Feb. 6, 2024

Actinidia arguta, known as hardy kiwifruit, is a widely cultivated species with distinct botanical characteristics such small and smooth-fruited, rich in beneficial nutrients, rapid softening tolerant to extremely low temperatures. It contains the most diverse ploidy types, including diploid, tetraploid, hexaploid, octoploid, decaploid. Here we report haplotype-resolved tetraploid genome (A. arguta cv. 'Longcheng No.2') containing four haplotypes, each 40,859, 41,377, 39,833 39,222 protein-coding genes. We described phased structure, synteny, evolutionary analyses identify date possible WGD events. K

Language: Английский

Citations

11
A High-Quality Phased Genome Assembly of Stinging Nettle (Urtica dioica ssp. dioica) DOI Creative Commons
Kaede Hirabayashi, Christopher R. Dumigan, Matúš Kučka

et al.

Plants, Journal Year: 2025, Volume and Issue: 14(1), P. 124 - 124

Published: Jan. 3, 2025

Stinging nettles (Urtica dioica) have a long history of association with human civilization, having been used as source textile fibers, food and medicine. Here, we present chromosome-level, phased genome assembly for diploid female clone Urtica dioica from Romania. Using combination PacBio HiFi, Oxford Nanopore, Illumina sequencing, well Hi-C long-range interaction data (using novel protocol presented here), assembled two haplotypes 574.9 Mbp (contig N50 = 10.9 Mbp, scaffold 44.0 Mbp) 521.2 13.5 48.0 Mbp), BUSCO scores 92.6% 92.2%. We annotated 20,333 20,140 genes each haplotype, covering over 90% the complete including copies gene putatively encoding neurotoxic peptide urthionin, which could contribute to nettle’s characteristic sting. Despite its relatively small size, nettle displays very high levels repetitiveness, transposable elements comprising more than 60% genome, considerable structural variation. This represents an important resource community will enable investigation genetic basis many interesting characteristics this species.

Language: Английский

Citations

1
A chromosome-scale reference assembly of Vigna radiata enables delineation of centromeres and telomeres DOI Creative Commons
Praveen Kumar Oraon, Heena Ambreen, Priyanka Yadav

et al.

Scientific Data, Journal Year: 2025, Volume and Issue: 12(1)

Published: Feb. 20, 2025

Vigna radiata (L.) R. Wilczek var. (mungbean) is a pulse crop important for both the global protein security and sustainable production. Here, to facilitate genomics-assisted breeding programs in mungbean, we present high-quality reference genome originating from crop's centre of origin, India. In this study, significantly continuous assembly V. Indian cultivar, achieved through combination long-read PacBio HiFi sequencing Hi-C sequencing. The total assembled size ~596 Mb equating ~98% predicted complemented by contig N50 value 10.35 BUSCO score 98.5%. Around 502 anchored on 11 pseudochromosomes conforming chromosome count with distinctly identified telomeres centromeres. We 43,147 gene models which 39,144 coding genes were functionally annotated. was able resolve several gaps provides genomic resource accelerating mungbean programs.

Language: Английский

Citations

1
Near chromosome-level and highly repetitive genome assembly of the snake pipefish Entelurus aequoreus (Syngnathiformes: Syngnathidae) DOI Creative Commons
Magnus Wolf, Bruno Lopes da Silva Ferrette, Raphael T. F. Coimbra

et al.

Gigabyte, Journal Year: 2024, Volume and Issue: 2024, P. 1 - 13

Published: Jan. 11, 2024

The snake pipefish,

Language: Английский

Citations

7
Telomere-to-telomere Genome Assembly of the Clubroot Pathogen Plasmodiophora Brassicae DOI Creative Commons
Muhammad Asim Javed, Soham Mukhopadhyay, Éric Normandeau

et al.

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(6)

Published: June 1, 2024

Plasmodiophora brassicae (Woronin, 1877), a biotrophic, obligate parasite, is the causal agent of clubroot disease in brassicas. The pathogen has been reported more than 80 countries worldwide, causing economic losses hundreds millions every year. Despite its widespread impact, very little known about molecular strategies it employs to induce characteristic clubs roots susceptible hosts during infection, nor mechanisms uses overcome genetic resistance. Here, we provide first telomere-to-telomere complete genome P. brassicae. We generated ∼27 Gb Illumina, Oxford Nanopore, and PacBio HiFi data from resting spores strain Pb3A produced 25.3 Mb assembly comprising 20 chromosomes, with an N50 1.37 Mb. BUSCO score, highest for any member group Rhizaria (Eukaryota: 88.2%), highlights limitations within Eukaryota database members this lineage. Using available transcriptomic protein evidence, annotated genome, identifying 10,521 protein-coding gene models. This high-quality, will serve as crucial resource plant pathology community advance much-needed understanding evolution pathogen.

Language: Английский

Citations

7
Genome sequence of the medicinal and ornamental plantDigitalis purpureareveals the molecular basis of flower color variation DOI Creative Commons
Jakob Maximilian Horz,

Katharina Wolff,

Ronja Friedhoff

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 15, 2024

Abstract Digitalis purpurea (foxglove) is a widely distributed ornamental plant and the producer of biomedical compound digoxin. Here, we present long read sequencing-based genome sequence red flowering D. corresponding prediction gene models. The high assembly continuity indicated by N50 4.3 Mbp completeness supported discovery about 96% complete BUSCO genes. This genomic resource paves way for an in-depth investigation flower pigmentation . Structural genes anthocyanin biosynthesis transcriptional regulators were identified. comparison white plants revealed large insertion in anthocyanidin synthase that most likely renders this non-functional could explain loss pigmentation. In addition, activator MYB5 shows 18 bp deletion results 6 amino acids protein. Furthermore, found DpTFL1/CEN to be responsible development terminal flowers.

Language: Английский

Citations

6