Perspective and Opportunity for forensic integrative genomics in the Human Pangenome Reference sequence era DOI Open Access
Guanglin He, Yuguo Huang, Jing Chen

et al.

Authorea (Authorea), Journal Year: 2023, Volume and Issue: unknown

Published: July 14, 2023

Human Pangenome Reference Consortium (HPRC) and Chinese (CPC) have pronounced the finish of pilot work Project, which aimed to build worldwide population-representative high-quality haplotype-resolved reference graph genomes. Graph-based gapless pangenome genomes with enriched genomic diversity higher completeness contiguity possessed potential for a new beginning third-generation sequencing (TGS)-based research high-performance mapping rate variant genotyping traditional short-read platforms. With coordinates corresponding computation algorithms methods, forensic integrative genomics fields will benefit in new-marker identification, highly-accurate marker genotyping, high-resolution panel development statistical algorithm updates. Here, we discussed past advances challenges pangenome-based their applications identification genomic, epigenetic, transcriptomic, microbiome practices. We highlighted necessity importance including TGS-based platforms, entire landscape diversity, study design graph-based NGS innovations achieve precision medicine.

Language: Английский

The complete sequence and comparative analysis of ape sex chromosomes DOI Creative Commons
Kateryna D. Makova, Brandon D. Pickett, Robert S. Harris

et al.

Nature, Journal Year: 2024, Volume and Issue: 630(8016), P. 401 - 411

Published: May 29, 2024

Abstract Apes possess two sex chromosomes—the male-specific Y chromosome and the X chromosome, which is present in both males females. The crucial for male reproduction, with deletions being linked to infertility 1 . vital reproduction cognition 2 Variation mating patterns brain function among apes suggests corresponding differences their chromosomes. However, owing repetitive nature incomplete reference assemblies, ape chromosomes have been challenging study. Here, using methodology developed telomere-to-telomere (T2T) human genome, we produced gapless assemblies of five great (bonobo ( Pan paniscus ), chimpanzee troglodytes western lowland gorilla Gorilla Bornean orangutan Pongo pygmaeus ) Sumatran abelii )) a lesser (the siamang gibbon Symphalangus syndactylus )), untangled intricacies evolution. Compared chromosomes, vary greatly size low alignability high levels structural rearrangements—owing accumulation lineage-specific ampliconic regions, palindromes, transposable elements satellites. Many genes expand multi-copy families some evolve under purifying selection. Thus, exhibits dynamic evolution, whereas more stable. Mapping short-read sequencing data these revealed diversity selection on than 100 individual apes. These are expected inform evolution conservation genetics non-human apes, all endangered species.

Language: Английский

Citations

59
Why do sex chromosomes progressively lose recombination? DOI
Paul Jay, Daniel L. Jeffries, Fanny E. Hartmann

et al.

Trends in Genetics, Journal Year: 2024, Volume and Issue: 40(7), P. 564 - 579

Published: April 27, 2024

Language: Английский

Citations

13
Origin and evolutionary trajectories of brown algal sex chromosomes DOI Creative Commons
Josué Barrera‐Redondo, Agnieszka P. Lipinska, Pengfei Liu

et al.

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

Published: Jan. 16, 2024

SUMMARY Sex chromosomes fall into three classes: XX/XY, ZW/ZZ and U/V systems. The rise, evolution demise of systems have remained enigmatic to date. Here, we analyze genomes spanning the entire brown algal phylogeny decipher their sex-determination evolutionary history. birth sex evolved more than 250 million years ago, when a pivotal male-determinant located in discrete region proto-U proto-V ceased recombining. Over time, nested inversions led step-wise expansions, accompanying increasing morphological complexity sexual differentiation seaweeds. Unlike XX/XY ZW/ZZ, evolve mainly by gene gain, showing minimal degeneration. They are structurally dynamic, act as genomic ’cradles’ fostering new genes. Our analyses show that hermaphroditism arose from ancestral males acquired U-specific genes ectopic recombination, transition an system, V-specific moved down genetic hierarchy determination. Both events lead U V erosion specific characteristics. Taken together, our findings offer comprehensive model chromosome evolution. HIGHLIGHTS Sexes algae due recombination male-determining gene-containing via gain ‘cradles’ novelty Emergence involved demotion V-master sex-determining Introgression female-specific male background allowed arise

Language: Английский

Citations

11
The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes DOI Creative Commons
Kateryna D. Makova, Brandon D. Pickett, Robert S. Harris

et al.

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

Published: Dec. 1, 2023

Abstract Apes possess two sex chromosomes—the male-specific Y and the X shared by males females. The chromosome is crucial for male reproduction, with deletions linked to infertility. carries genes vital reproduction cognition. Variation in mating patterns brain function among great apes suggests corresponding differences their structure evolution. However, due highly repetitive nature incomplete reference assemblies, ape chromosomes have been challenging study. Here, using state-of-the-art experimental computational methods developed telomere-to-telomere (T2T) human genome, we produced gapless, complete assemblies of five (chimpanzee, bonobo, gorilla, Bornean Sumatran orangutans) a lesser ape, siamang gibbon. These completely resolved ampliconic, palindromic, satellite sequences, including entire centromeres, allowing us untangle intricacies We found that, compared X, vary greatly size low alignability high levels structural rearrangements. This divergence on arises from accumulation lineage-specific ampliconic regions palindromes (which are more broadly species X) abundance transposable elements satellites lower representation X). Our analysis revealed expansions multi-copy gene families signatures purifying selection. In summary, exhibits dynamic evolution, while stable. Finally, mapping short-read sequencing data >100 individuals diversity selection chromosomes, demonstrating utility these studies expected further inform conservation genetics nonhuman apes, all which endangered species.

Language: Английский

Citations

11
Structural variation in humans and our primate kin in the era of telomere-to-telomere genomes and pangenomics DOI Creative Commons

Joana L. Rocha,

Runyang Nicolas Lou, Peter H. Sudmant

et al.

Current Opinion in Genetics & Development, Journal Year: 2024, Volume and Issue: 87, P. 102233 - 102233

Published: July 23, 2024

Structural variants (SVs) account for the majority of base pair differences both within and between primate species. However, our understanding inter- intra-species SV has been historically hampered by quality draft genomes absence genome resources key taxa. Recently, advances in long-read sequencing assembly have begun to radically reshape SVs. Two landmark achievements include publication a human telomere-to-telomere (T2T) as well development first pangenome reference. In this review, we look back major works laying foundation these projects. We then examine ways which T2T assemblies pangenomes are transforming approach SV. Finally, discuss what future research may like era pangenomics.

Language: Английский

Citations

4
Comparative genomics illuminates karyotype and sex chromosome evolution of sharks DOI Creative Commons
Jiahong Wu, Fujiang Liu, Jie Jiao

et al.

Cell Genomics, Journal Year: 2024, Volume and Issue: 4(8), P. 100607 - 100607

Published: July 11, 2024

Chondrichthyes is an important lineage to reconstruct the evolutionary history of vertebrates. Here, we analyzed genome synteny for six chondrichthyan chromosome-level genomes. Our comparative analysis reveals a slow rate chromosomal changes, with infrequent but independent fusions observed in sharks, skates, and chimaeras. The common ancestor had proto-vertebrate-like karyotype, including presence 18 microchromosome pairs. X chromosome conversed shared by all suggesting likely origin sex at least 181 million years ago. We characterized Y chromosomes two sharks that are highly differentiated from except small young stratum pseudoautosomal region. found shark lack global dosage compensation dosage-sensitive genes locally compensated. study on evolution enhances our understanding vertebrate evolution.

Language: Английский

Citations

3
YHSeqY3000 panel captures all founding lineages in the Chinese paternal genomic diversity database DOI Creative Commons
Mengge Wang,

Shuhan Duan,

Qiuxia Sun

et al.

BMC Biology, Journal Year: 2025, Volume and Issue: 23(1)

Published: Jan. 21, 2025

The advancements in second-/third-generation sequencing technologies, alongside computational innovations, have significantly enhanced our understanding of the genomic structure Y-chromosomes and their unique phylogenetic characteristics. These researches, despite challenges posed by lack population-scale databases, potential to revolutionize approach high-resolution, population-specific Y-chromosome panels databases for anthropological forensic applications. This study aimed develop highest-resolution Y-targeted panel, utilizing time-stamped, core informative mutations identified from high-coverage sequences YanHuang cohort. panel is intended provide a new tool complex pedigree search paternal biogeographical ancestry inference, as well explore general patterns fine-scale evolutionary history ethnolinguistically diverse Chinese populations. performance East Asian-specific Y-chromosomal including 2999-core SNP variants, was found be robust reliable. YHSeqY3000 designed capture genetic diversity lineages 3500 years ago, identifying 408 terminal 2097 individuals across 41 genetically geographically distinct We substructure that correlating with ancient population migrations expansions. New evidence provided extensive gene flow events between minority ethnic groups Han people, based on integrative Paternal Genomic Diversity Database. work successfully integrated Y-chromosome-related basic science translational applications, emphasizing necessity comprehensively characterizing genomically under-representative particularly important second phase medical or cohorts, where dense sampling strategies are employed.

Language: Английский

Citations

0
Evolutionary divergence between homologous X–Y chromosome genes shapes sex-biased biology DOI

Alex R. DeCasien,

Kathryn Tsai, Siyuan Liu

et al.

Nature Ecology & Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 24, 2025

Language: Английский

Citations

0
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

Citations

0
Multiple origins and phenotypic implications of an extended human pseudoautosomal region shown by analysis of the UK Biobank DOI Creative Commons
Nitikorn Poriswanish, James Eales, Xiaoguang Xu

et al.

The American Journal of Human Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 1, 2025

Language: Английский

Citations

0