Genome assembly in the telomere-to-telomere era

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

Published: April 22, 2024

Language: Английский

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Rapid and dynamic evolution of a giant Y chromosome in Silene latifolia

Science, Journal Year: 2025, Volume and Issue: 387(6734), P. 637 - 643

Published: Feb. 6, 2025

Some plants have massive sex-linked regions. To test hypotheses about their evolution, we sequenced the genome of Silene latifolia , in which giant heteromorphic sex chromosomes were first discovered 1923. It has long been known that Y chromosome consists mainly a male-specific region does not recombine with X and carries sex-determining genes other male functions. However, only whole assembly can candidate be validated experimentally locations determined related to suppression recombination. We describe genomic changes as ancestral evolved into current XY pair, testing ideas evolution large nonrecombining regions mechanisms created present recombination pattern.

Language: Английский

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Recent Advances in Generative Adversarial Networks for Gene Expression Data: A Comprehensive Review

Mathematics, Journal Year: 2023, Volume and Issue: 11(14), P. 3055 - 3055

Published: July 10, 2023

The evolving field of generative artificial intelligence (GenAI), particularly deep learning, is revolutionizing a host scientific and technological sectors. One the pivotal innovations within this domain emergence adversarial networks (GANs). These unique models have shown remarkable capabilities in crafting synthetic data, closely emulating real-world distributions. Notably, their application to gene expression data systems fascinating rapidly growing focus area. Restrictions related ethical logistical issues often limit size, diversity, data-gathering speed data. Herein lies potential GANs, as they are capable producing offering solution these limitations. This review provides thorough analysis most recent advancements at innovative crossroads GANs specifically during period from 2019 2023. In context fast-paced progress learning technologies, accurate inclusive reviews current practices critical guiding subsequent research efforts, sharing knowledge, catalyzing continual growth discipline. review, through highlighting studies seminal works, serves key resource for academics professionals alike, aiding journey compelling confluence systems.

Language: Английский

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Ancient diversity in host-parasite interaction genes in a model parasitic nematode

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Nov. 27, 2023

Host-parasite interactions exert strong selection pressures on the genomes of both host and parasite. These can lead to negative frequency-dependent selection, a form balancing that is hypothesised explain high levels polymorphism seen in many immune parasite antigen loci. Here, we sequence several individuals Heligmosomoides bakeri, model house mice, polygyrus, closely related wood mice. Although H. bakeri commonly referred as polygyrus literature, their show divergence are consistent with at least million years independent evolution. The species contain hyper-divergent haplotypes enriched for proteins interact response. Many these originated prior between suggesting they have been maintained by long-term selection. Together, our results suggest exerted response played key role shaping patterns genetic diversity parasitic nematodes.

Language: Английский

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Phased Assembly of Neo-Sex Chromosomes Reveals Extensive Y Degeneration and Rapid Genome Evolution in Rumex hastatulus

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(4)

Published: April 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.

Language: Английский

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The genome sequence of the giant clam, Tridacna gigas (Linnaeus, 1758)

Wellcome Open Research, Journal Year: 2024, Volume and Issue: 9, P. 145 - 145

Published: March 19, 2024

We present a chromosomal-level genome assembly from an individual Tridacna gigas (the giant clam; Mollusca; Bivalvia; Veneroida; Cardiidae). The sequence is 1,175.9 megabases in span. Most of the scaffolded into 17 chromosomal pseudomolecules. mitochondrial has also been assembled and 25.34 kilobases length. Gene annotation this on Ensembl identified 18,177 protein coding genes.

Language: Английский

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Chromosome-level scaffolding of haplotype-resolved assemblies using Hi-C data without reference genomes

Nature Plants, Journal Year: 2024, Volume and Issue: 10(8), P. 1184 - 1200

Published: Aug. 5, 2024

Language: Английский

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A candidate sex determination locus in amphibians which evolved by structural variation between X- and Y-chromosomes

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: June 5, 2024

Abstract Most vertebrates develop distinct females and males, where sex is determined by repeatedly evolved environmental or genetic triggers. Undifferentiated chromosomes large genomes have caused major knowledge gaps in amphibians. Only a single master sex-determining gene, the dmrt1 -paralogue ( dm-w ) of female-heterogametic clawed frogs Xenopus ; ZW♀/ZZ♂), known across >8740 species In this study, combining chromosome-scale female male non-model amphibian, European green toad, Bufo tes viridis , with ddRAD- whole genome pool-sequencing, we reveal candidate locus, governing male-heterogametic system (XX♀/XY♂). Targeted sequencing multiple taxa uncovered structural X/Y-variation 5′-regulatory region gene bod1l Y-specific non-coding RNA (ncRNA-Y), only expressed suggests that locus initiates sex-specific differentiation. Developmental transcriptomes in-situ hybridization show timely spatially relevant ncRNA-Y -gene expression primordial gonads. This coincided differential H3K4me -methylation pre-granulosa/pre-Sertoli cells, pointing to specific mechanism amphibian determination.

Language: Английский

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Chromosome-level genome assembly of Salvia sclarea

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

Published: Jan. 4, 2025

Salvia sclarea is a medicinal herb from the Lamiaceae family, valued for its essential oil which contains sclareol, linalool, linalyl acetate, and other compounds. Despite extensive use, genetic mechanisms of S. are not well understood. This study presents chromosome-level genome assembly using Oxford Nanopore Technology, Illumina short reads, Pore-C technology. The assembled spans 499.03 Mbp with scaffold N50 50.5 Mbp, forming 11 pseudochromosomes. was validated by BUSCO analysis, indicated high completeness marked at 98.7%. 68.73% repetitive sequences, long terminal repeats (LTRs) accounting 33.01%. A total 17,202 protein-coding genes were predicted. Among them, 16,846 annotated in NCBI NR database, highest among all databases, covering 97.93% predicted genes. phylogenetic analysis revealed that shares close evolutionary relationship officinalis within genus, while species genus have evolved independently family. high-resolution offers fresh insights into biosynthesis oils aromatic compounds sclarea, establishing basis preservation.

Language: Английский

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Chromosome-scale telomere to telomere genome assembly of common crystalwort (Riccia sorocarpa Bisch.)

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

Published: Jan. 15, 2025

Abstract Riccia sorocarpa Bisch., commonly known as common crystalwort, is a plant belonging to the Marchantiales order with cosmopolitan distribution among wide range of habitats: fields, gardens, waste ground, on paths, cliff tops, and thin soil over rocks or by water bodies. However, research into genetic aspects this species limited. In study, chromosome-scale telomere-to-telomere genome R. was assembled exclusively Oxford Nanopore long-read sequencing Pore-C technology. A high-quality chromosomal-scale assembly obtained final size 376.690 Mbp, contig N50 49.132 Mbp 97.02% contigs associated eight chromosomes. Genome completeness confirmed BUSCO analysis accounting 91.8%. Among 27,626 total genes, 23,562 (85.29%) were functionally annotated. Moreover, collinearity analyzed well gene family evolution DNA methylation profile. The availability genome, which second liverwort assembly, opens up new avenues for in-depth diversity genomic characteristics.

Language: Английский

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