Incomplete lineage sorting of segmental duplications defines the human chromosome 2 fusion site early during African great ape speciation DOI Creative Commons
Xinrui Jiang, Lu Zhang, Zikun Yang

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Дек. 17, 2024

ABSTRACT All great apes differ karyotypically from humans due to the fusion of chromosomes 2a and 2b, resulting in human chromosome 2. Yet, structure, function, evolutionary history genomic regions associated with this remain poorly understood. Here, we analyze finished telomere-to-telomere macaques show that was multiple pericentric inversions, segmental duplications (SDs), rapid turnover subterminal repetitive DNA. We characterized site at single-base-pair resolution identified three distinct SDs originated more than 5 million years ago. These were differentially distributed among African as a result incomplete lineage sorting (ILS) lineage-specific duplication. Most conspicuously, one these shares homology hypomethylated SD spacer sequence present hundreds copies heterochromatin chimpanzees bonobos. The accompanied by systematic degradation divergent α-satellite arrays representing ancestral centromere creating five structural haplotypes humans. CRISPR/Cas9-mediated depletion cell lines significantly alters expression 108 genes, indicating potential regulatory consequence human-specific karyotypic change.

Язык: Английский

Genome-scale evolution in local populations of wild chimpanzees DOI Creative Commons
Takashi Hayakawa, Takushi Kishida, Yasuhiro Go

и другие.

Scientific Reports, Год журнала: 2025, Номер 15(1)

Опубликована: Янв. 2, 2025

Язык: Английский

Процитировано

1
Integrated analysis of the complete sequence of a macaque genome DOI
Shilong Zhang, Ning Xu,

Lianting Fu

и другие.

Nature, Год журнала: 2025, Номер unknown

Опубликована: Фев. 26, 2025

Язык: Английский

Процитировано

1
Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon DOI Creative Commons
Gabrielle A. Hartley, Mariam Okhovat, Savannah J. Hoyt

и другие.

Cell Genomics, Год журнала: 2025, Номер unknown, С. 100808 - 100808

Опубликована: Март 1, 2025

Язык: Английский

Процитировано

1
wgatools: an ultrafast toolkit for manipulating whole-genome alignments DOI Creative Commons
Wenjie Wei, Songtao Gui, Jian Yang

и другие.

Bioinformatics, Год журнала: 2025, Номер 41(4)

Опубликована: Март 27, 2025

Summary: With the rapid development of long-read sequencing technologies, era individual complete genomes is approaching. We have developed wgatools, a cross-platform, ultrafast toolkit that supports range whole genome alignment (WGA) formats, offering practical tools for conversion, processing, statistical evaluation, and visualization alignments, thereby facilitating population-level analysis advancing functional evolutionary genomics. Availability Implementation: wgatools diverse formats can process, filter, statistically evaluate perform alignment-based variant calling, visualize alignments both locally genome-wide. Built with Rust efficiency safe memory usage, it ensures fast performance handle large datasets consisting hundreds genomes. published as free software under MIT open-source license, its source code freely available at https://github.com/wjwei-handsome/wgatools. Contact: [email protected] (W.W.) or [email protected] (H.-J.L.).

Язык: Английский

Процитировано

0
PanTE: A Comprehensive Framework for Transposable Element Discovery in Graph-based Pangenomes DOI Creative Commons
Yiwen Wang, Shuo Cao, Zhenya Liu

и другие.

Research Square (Research Square), Год журнала: 2025, Номер unknown

Опубликована: Фев. 5, 2025

Abstract Transposable element (TE) annotation is crucial for understanding genetics, genomics and evolution, yet current methods struggle to identify TEs in graph-based pangenomes. We developed a framework PanTE construct accurate representative TE libraries both single genomes graph the first of its kind capable being directly applied pangenomes build population-level libraries. By partially reimplementing RepeatModeler2 integrating key innovations, including pangenome disassembly, alignment-free LTR structure detection, machine learning-based classifier efficiency-boosting strategies, outperformed by efficiently handling large genomes, detecting high-abundance LTR-retrotransposons, providing robust classification with superior computational efficiency. Compared EDTA, it annotated ~ 26% more grapevine genome achieved up 13 times faster runtimes wheat genome. represents significant advancement population-wide discovery, making particularly valuable pangenomic studies.

Язык: Английский

Процитировано

0
Advancing evolutionary medicine with complete primate genomes and advanced biotechnologies DOI
Kaiyue Ma, Xiangyu Yang, Yafei Mao

и другие.

Trends in Genetics, Год журнала: 2024, Номер unknown

Опубликована: Дек. 1, 2024

Язык: Английский

Процитировано

3
Non-canonical DNA in human and other ape telomere-to-telomere genomes DOI Creative Commons
Linnéa Smeds,

Kaivan Kamali,

Iva Kejnovská

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Сен. 3, 2024

Abstract Non-canonical (non-B) DNA structures—e.g., bent DNA, hairpins, G-quadruplexes, Z-DNA, etc.—which form at certain sequence motifs (e.g., A-phased repeats, inverted etc.), have emerged as important regulators of cellular processes and drivers genome evolution. Yet, they been understudied due to their repetitive nature potentially inaccurate sequences generated with short-read technologies. Here we comprehensively characterize such in the long-read telomere-to-telomere (T2T) genomes human, bonobo, chimpanzee, gorilla, Bornean orangutan, Sumatran siamang. Non-B are enriched genomic regions added T2T assemblies, occupy 9-15%, 9-11%, 12-38% autosomes, chromosomes X Y, respectively. Functional promoters enhancers) non-B motifs. concentrate short arms acrocentric a pattern reflecting satellite repeat content might contribute dynamics these regions. Most centromeres and/or flanking least one motif type, consistent potential role structures determining centromeres. Our results highlight uneven distribution predicted across ape suggest novel functions previously inaccessible Graphical

Язык: Английский

Процитировано

1
Gene expansions contributing to human brain evolution DOI Creative Commons
Daniela C. Soto, José M. Uribe‐Salazar, Gulhan Kaya

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Сен. 26, 2024

Genomic drivers of human-specific neurological traits remain largely undiscovered. Duplicated genes expanded uniquely in the human lineage likely contributed to brain evolution, including increased complexity synaptic connections between neurons and dramatic expansion neocortex. Discovering duplicate is challenging because similarity paralogs makes them prone sequence-assembly errors. To mitigate this issue, we analyzed a complete telomere-to-telomere genome sequence (T2T-CHM13) identified 213 duplicated gene families containing (>98% identity). Positing that important universal features should exist with at least one copy all modern humans exhibit expression brain, narrowed on 362 across thousands ancestrally diverse genomes present transcriptomes. Of these, 38 co-express modules enriched for autism-associated potentially contribute language cognition. We 13 are fixed among show convincing patterns. Using long-read DNA sequencing revealed hidden variation 200 ancestries, uncovering signatures selection not previously identified, possible balancing

Язык: Английский

Процитировано

1
LINE1 elements at distal junctions of rDNA repeats regulate nucleolar organization in human embryonic stem cells DOI Open Access

Lamisa Ataei,

Juan Zhang,

Simon Monis

и другие.

Genes & Development, Год журнала: 2024, Номер 39(3-4), С. 280 - 298

Опубликована: Дек. 20, 2024

The nucleolus is a major subnuclear compartment where ribosomal DNA (rDNA) transcribed and ribosomes are assembled. In addition, recent studies have shown that the dynamic organizer of chromatin architecture modulates developmental gene expression. rDNA units assembled into arrays located in p-arms five human acrocentric chromosomes. Distal junctions (DJs) ∼400 kb sequences adjacent to thought anchor them at nucleolus, although underlying regulatory elements remain unclear. Here we show DJs display chromosome conformation profile embryonic stem cells (hESCs). We identified primate-specific, full-length insertion retrotransposon long interspersed nuclear element 1 (LINE1) conserved position across all DJs. This DJ-LINE1 locus interacts with specific regions DJ upregulated naïve hESCs. CRISPR-based deletion interference approaches revealed contributes nucleolar positioning Moreover, found expression required for maintenance structure transcriptional output Silencing leads loss self-renewal, disruption landscape accessibility, derepression earlier programs work uncovers LINE1 fundamental role organization hESCs provides new insights how functions as key genome-organizing hub.

Язык: Английский

Процитировано

1
Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon DOI Creative Commons
Gabrielle A. Hartley, Mariam Okhovat, Savannah J. Hoyt

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Авг. 30, 2024

Great apes have maintained a stable karyotype with few large-scale rearrangements; in contrast, gibbons undergone high rate of chromosomal rearrangements coincident rapid centromere turnover. Here we characterize assembled centromeres the Eastern hoolock gibbon,

Язык: Английский

Процитировано

0