Silver chimaera genome assembly and identification of the holocephalan sex chromosome sequence DOI Creative Commons
Akinori Teramura, Mitsutaka Kadota, Shotaro Hirase

и другие.

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

Опубликована: Авг. 20, 2024

Abstract Cartilaginous fishes are divided into holocephalans and elasmobranchs, comparative studies involving them expected to elucidate how variable phenotypes distinctive genomic properties were established in those ancient vertebrate lineages. To date, molecular-level on have concentrated the family Callorhinchidae, with a chromosome-scale genome assembly of Callorhinchus milii available. In this study, we focused most species-rich holocephalan Chimaeridae sequenced its member, silver chimaera ( Chimaera phantasma ). We report first Chimaeridae, high continuity completeness, which exhibited large intragenomic variation chromosome lengths, is correlated intron size. This pattern observed more widely vertebrates at least partly accounts for cross-species size variation. A male-female comparison identified scaffold double sequence depth females, identify as an X fragment. DNA sequence-based evidence sex chromosome, suggesting male heterogametic determination system. allowing chromosome-level among genomes, will trigger in-depth understanding diversity well species’ population genetic structures based completeness.

Язык: Английский

Evolutionary divergence in CTCF-mediated chromatin topology drives transcriptional innovation in humans DOI Creative Commons
Xia Wu, Dan Xiong, Rong Liu

и другие.

Nature Communications, Год журнала: 2025, Номер 16(1)

Опубликована: Март 26, 2025

Chromatin topology can impact gene regulation, but how evolutionary divergence in chromatin has shaped regulatory landscapes for distinctive human traits remains poorly understood. CTCF sites determine by forming domains and loops. Here, we show CTCF-mediated at the domain loop scales during primate evolution, elucidating distinct mechanisms shaping landscapes. Human-specific divergent lead to a broad rewiring of transcriptional Divergent loops concord with species-specific enhancer activity, influencing connectivity target genes concordant yet constrained manner. Under this mechanism, establish role human-specific isoform diversity, functional implications disease susceptibility. Furthermore, validate function these using forebrain organoids. This study advances our understanding genetic evolution from perspective genome architecture. regulation. Wu et al. that changes structure, particularly loops, drive diversity contributing traits.

Язык: Английский

Процитировано

1
Function and Evolution of the Loop Extrusion Machinery in Animals DOI Open Access
Evelyn Kabirova, Artem Nurislamov, Artem Shadskiy

и другие.

International Journal of Molecular Sciences, Год журнала: 2023, Номер 24(5), С. 5017 - 5017

Опубликована: Март 6, 2023

Structural maintenance of chromosomes (SMC) complexes are essential proteins found in genomes all cellular organisms. Essential functions these proteins, such as mitotic chromosome formation and sister chromatid cohesion, were discovered a long time ago. Recent advances chromatin biology showed that SMC involved many other genomic processes, acting active motors extruding DNA, which leads to the loops. Some loops formed by highly cell type developmental stage specific, SMC-mediated DNA required for VDJ recombination B-cell progenitors, or dosage compensation Caenorhabditis elegans X-chromosome inactivation mice. In this review, we focus on extrusion-based mechanisms common multiple types species. We will first describe an anatomy their accessory proteins. Next, provide biochemical details extrusion process. follow sections describing role gene regulation, repair, topology.

Язык: Английский

Процитировано

21
The hagfish genome and the evolution of vertebrates DOI Creative Commons
Ferdinand Marlétaz, Nataliya Timoshevskaya, Vladimir A. Timoshevskiy

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Апрель 18, 2023

Abstract As the only surviving lineages of jawless fishes, hagfishes and lampreys provide a critical window into early vertebrate evolution. Here, we investigate complex history, timing, functional role genome-wide duplications in vertebrates light chromosome-scale genome brown hagfish Eptatretus atami . Using robust (paralogon-based) phylogenetic methods, confirm monophyly cyclostomes, document an auto-tetraploidization (1R V ) that predated origin crown group ∼517 Mya, establish timing subsequent independent gnathostome cyclostome lineages. Some 1R gene can be linked to key innovations, suggesting this genomewide event contributed emergence pan-vertebrate features such as neural crest. The karyotype is derived by numerous fusions relative ancestral arrangement preserved lampreys. These genomic changes were accompanied loss genes essential for organ systems (eyes, osteoclast) are absent hagfish, accounting part simplification body plan; other family expansions account hagfishes’ capacity produce slime. Finally, characterise programmed DNA elimination somatic cells identifying protein-coding repetitive elements deleted during development. lampreys, these provides mechanism resolving genetic conflict between soma germline repressing germline/pluripotency functions. Reconstruction history framework further exploration novelties.

Язык: Английский

Процитировано

16
Convergent gene losses and pseudogenizations in multiple lineages of stomachless fishes DOI Creative Commons
Akira Kato,

Supriya Pipil,

Chihiro Ota

и другие.

Communications Biology, Год журнала: 2024, Номер 7(1)

Опубликована: Апрель 3, 2024

Abstract The regressive evolution of independent lineages often results in convergent phenotypes. Several teleost groups display secondary loss the stomach, and four gastric genes, atp4a , atp4b pgc pga2 have been co-deleted agastric (stomachless) fish. Analyses genotypic convergence among fishes showed that slc26a9 kcne2 cldn18a vsig1 were or pseudogenized most major groups. also deleted monotreme echidna platypus, respectively. In stomachs sticklebacks, these genes are expressed gland cells surface epithelial cells. An ohnolog cldn18 was retained some teleosts but exhibited an increased non-synonymous substitution when compared with species. These revealed novel gene losses at multiple loci fish, as well a single platypus.

Язык: Английский

Процитировано

6
Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization DOI Creative Commons
Kazuaki Yamaguchi, Yoshinobu Uno, Mitsutaka Kadota

и другие.

Genome Research, Год журнала: 2023, Номер 33(9), С. 1527 - 1540

Опубликована: Авг. 17, 2023

Genomic studies of vertebrate chromosome evolution have long been hindered by the scarcity chromosome-scale DNA sequences some key taxa. One those limiting taxa has elasmobranchs (sharks and rays), which harbor species often with numerous chromosomes enlarged genomes. Here, we report genome assembly for zebra shark Stegostoma tigrinum, an endangered that a relatively small among sharks (3.71 Gb), as well whale Rhincodon typus Our analysis using male-female comparison identified X Chromosome, first genomically characterized sex chromosome. The Chromosome harbors Hox C cluster whose intact linkage not shown elasmobranch fish. sequenced genomes show gradualism length remarkable length-dependent characteristics-shorter tend to higher GC content, gene density, synonymous substitution rate, simple tandem repeat content smaller lower interspersed content. We challenge traditional binary classification karyotypes without so-called microchromosomes. Even microchromosomes, characteristics persist widely in nonmammalian vertebrates. investigation underpins their unique provides clues understanding how accommodate intragenomic heterogeneity realize complex readout. It also paves way dissecting more variable sizes be at high quality.

Язык: Английский

Процитировано

13
A review of BioTree construction in the context of information fusion: Priors, methods, applications and trends DOI
Zelin Zang, Yongjie Xu,

Chenrui Duan

и другие.

Information Fusion, Год журнала: 2025, Номер unknown, С. 103108 - 103108

Опубликована: Март 1, 2025

Язык: Английский

Процитировано

0
Evolution of the batoidea pectoral fin skeleton: convergence, modularity, and integration driving disparity trends DOI Creative Commons
Faviel A. López‐Romero, Eduardo Villalobos‐Segura, Julia Türtscher

и другие.

Evolutionary Ecology, Год журнала: 2025, Номер unknown

Опубликована: Фев. 17, 2025

Язык: Английский

Процитировано

0
Evolutionary trends in the elasmobranch neurocranium DOI Creative Commons
Joel H. Gayford, Martin Brazeau, Gavin J. P. Naylor

и другие.

Scientific Reports, Год журнала: 2024, Номер 14(1)

Опубликована: Май 20, 2024

Abstract The neurocranium (braincase) is one of the defining vertebrate characters. Housing brain and other key sensory organs, articulating with jaws contributing to shape anteriormost portion body, braincase undoubtedly great functional importance. Through studying relationships between ecology we can gain an improved understanding form-function in extant fossil taxa. Elasmobranchii (sharks rays) represent important case study diversity as their simplified somewhat decoupled from components cranium relative vertebrates. Little known about associations this clade. In report patterns mosaic cranial evolution that differ significantly those present clades. degree evolutionary modularity also differs Selachii Batoidea. both cases innovation jaw suspension appears have driven shifts integration modularity, subsequently facilitating ecological diversification. Our results confirm importance water depth biogeography drivers elasmobranch indicate skeletal articulation represents a major constraint upon

Язык: Английский

Процитировано

3
Comparative genomics illuminates karyotype and sex chromosome evolution of sharks DOI Creative Commons
Jiahong Wu, Fujiang Liu, Jie Jiao

и другие.

Cell Genomics, Год журнала: 2024, Номер 4(8), С. 100607 - 100607

Опубликована: Июль 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.

Язык: Английский

Процитировано

3
Functional associations of evolutionarily recent human genes exhibit sensitivity to the 3D genome landscape and disease DOI Creative Commons

Katherine Fleck,

Victor Luria,

Nitanta Garag

и другие.

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

Опубликована: Март 17, 2024

Summary Genome organization is intricately tied to regulating genes and associated cell fate decisions. Here, we examine the positioning functional significance of human genes, grouped by their lineage restriction level, within 3D genome. We reveal that different levels have distinct relationships with both domains loop anchors, remarkably consistent boundaries across types. While associations each group are primarily type-specific, conserved maintain greater stability genomic features disease than recently evolved genes. Furthermore, expression these various tissues follows an evolutionary progression, such RNA increase from young restricted ancient present in most species. Thus, gene age, function, contribute tissue-specific regulation development disease.

Язык: Английский

Процитировано

2