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

и другие.

Nature, Год журнала: 2024, Номер 630(8016), С. 401 - 411

Опубликована: Май 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.

Язык: Английский

DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer DOI
Gunjan Baid, Daniel E. Cook, Kishwar Shafin

и другие.

Nature Biotechnology, Год журнала: 2022, Номер unknown

Опубликована: Сен. 1, 2022

Язык: Английский

Процитировано

100

DiMeLo-seq: a long-read, single-molecule method for mapping protein–DNA interactions genome wide DOI
Nicolas Altemose, Annie Maslan, Owen K. Smith

и другие.

Nature Methods, Год журнала: 2022, Номер 19(6), С. 711 - 723

Опубликована: Апрель 8, 2022

Язык: Английский

Процитировано

94

Cycles of satellite and transposon evolution in Arabidopsis centromeres DOI
Piotr Włodzimierz, Fernando A. Rabanal, Robin Burns

и другие.

Nature, Год журнала: 2023, Номер 618(7965), С. 557 - 565

Опубликована: Май 17, 2023

Язык: Английский

Процитировано

93

Evolutionary analysis of a complete chicken genome DOI Creative Commons
Zhen Huang,

Zaoxu Xu,

Hao Bai

и другие.

Proceedings of the National Academy of Sciences, Год журнала: 2023, Номер 120(8)

Опубликована: Фев. 13, 2023

Microchromosomes are prevalent in nonmammalian vertebrates [P. D. Waters et al. , Proc. Natl. Acad. Sci. U.S.A. 118 (2021)], but a few of them missing bird genome assemblies. Here, we present new chicken reference containing all autosomes, Z and W chromosome, with gaps closed except for the W. We identified ten small microchromosomes (termed dot chromosomes) distinct sequence epigenetic features, among which six were newly assembled. Those chromosomes exhibit extremely high GC content level DNA methylation enriched housekeeping genes. The pericentromeric heterochromatin is disproportionately large continues to expand proliferation satellite testis-expressed Our analyses revealed that 41-bp CNM repeat frequently forms higher-order repeats (HORs) at centromeres acrocentric chromosomes. centromere core regions where kinetochore attaches often encompass telomeric (TTAGGG)n, one chromosomes, recruits an endogenous retrovirus (ERV). further demonstrate chromosome shares some common features having arrays hypermethylated tandem repeats. Finally, using complete models, reconstructed fine picture chordate karyotype evolution, revealing frequent chromosomal fusions before after vertebrate whole-genome duplications. characterization shed insights into understanding evolution biology.

Язык: Английский

Процитировано

89

Variant calling and benchmarking in an era of complete human genome sequences DOI
Nathan D. Olson, Justin Wagner, Nathan Dwarshuis

и другие.

Nature Reviews Genetics, Год журнала: 2023, Номер 24(7), С. 464 - 483

Опубликована: Апрель 14, 2023

Язык: Английский

Процитировано

81

Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies DOI
Ann M. Mc Cartney, Kishwar Shafin, Michael Alonge

и другие.

Nature Methods, Год журнала: 2022, Номер 19(6), С. 687 - 695

Опубликована: Март 31, 2022

Язык: Английский

Процитировано

77

Genomics in the long-read sequencing era DOI Creative Commons

Erwin L. van Dijk,

Delphine Naquin, Kévin Gorrichon

и другие.

Trends in Genetics, Год журнала: 2023, Номер 39(9), С. 649 - 671

Опубликована: Май 23, 2023

Язык: Английский

Процитировано

74

A Draft Human Pangenome Reference DOI Creative Commons
Wen‐Wei Liao, Mobin Asri, Jana Ebler

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2022, Номер unknown

Опубликована: Июль 9, 2022

Abstract The Human Pangenome Reference Consortium (HPRC) presents a first draft human pangenome reference. contains 47 phased, diploid assemblies from cohort of genetically diverse individuals. These cover more than 99% the expected sequence and are accurate at structural base-pair levels. Based on alignments assemblies, we generated that captures known variants haplotypes, reveals novel alleles structurally complex loci, adds 119 million base pairs euchromatic polymorphic 1,529 gene duplications relative to existing reference, GRCh38. Roughly 90 additional derive variation. Using our analyze short-read data reduces errors when discovering small by 34% boosts detected per haplotype 104% compared GRCh38-based workflows, using previous diversity sets genome assemblies.

Язык: Английский

Процитировано

73

The variation and evolution of complete human centromeres DOI Creative Commons
Glennis A. Logsdon, Allison N. Rozanski, Fedor Ryabov

и другие.

Nature, Год журнала: 2024, Номер 629(8010), С. 136 - 145

Опубликована: Апрель 3, 2024

Abstract Human centromeres have been traditionally very difficult to sequence and assemble owing their repetitive nature large size 1 . As a result, patterns of human centromeric variation models for evolution function remain incomplete, despite being among the most rapidly mutating regions 2,3 Here, using long-read sequencing, we completely sequenced assembled all from second genome compared it finished reference 4,5 We find that two sets show at least 4.1-fold increase in single-nucleotide when with unique flanks vary up 3-fold size. Moreover, 45.8% cannot be reliably aligned standard methods emergence new α-satellite higher-order repeats (HORs). DNA methylation CENP-A chromatin immunoprecipitation experiments 26% differ kinetochore position by >500 kb. To understand evolutionary change, selected six chromosomes 31 orthologous common chimpanzee, orangutan macaque genomes. Comparative analyses reveal nearly complete turnover HORs, characteristic idiosyncratic changes HORs each species. Phylogenetic reconstruction haplotypes supports limited no recombination between short (p) long (q) arms across reveals novel share monophyletic origin, providing strategy estimate rate saltatory amplification mutation DNA.

Язык: Английский

Процитировано

71

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

Nature Reviews Genetics, Год журнала: 2024, Номер 25(9), С. 658 - 670

Опубликована: Апрель 22, 2024

Язык: Английский

Процитировано

69