Fish & Shellfish Immunology, Journal Year: 2024, Volume and Issue: 147, P. 109431 - 109431
Published: Feb. 10, 2024
Language: Английский
Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(9)
Published: Aug. 13, 2024
Abstract The organization of genomes into chromosomes is critical for processes such as genetic recombination, environmental adaptation, and speciation. All animals with bilateral symmetry inherited a genome structure from their last common ancestor that has been highly conserved in some taxa but seemingly unconstrained others. However, the evolutionary forces driving these differences by which they emerge have remained largely uncharacterized. Here, we analyze across phylum Annelida using 23 chromosome-level annelid genomes. We find while many lineages maintained bilaterian structure, Clitellata, group containing leeches earthworms, possesses completely scrambled develop rearrangement index to quantify extent evolution show that, compared bilaterians, earthworms among most rearranged any currently sampled species. further can be classified two distinct categories—high low rearrangement—largely influenced presence or absence, respectively, chromosome fission events. Our findings demonstrate animal variable within reveal occur both gradual, stepwise fashion, rapid, all-encompassing changes over short timescales.
Language: Английский
Citations
11
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: Feb. 16, 2024
Abstract Groups of orthologous genes are commonly found together on the same chromosome over vast evolutionary distances. This extensive physical gene linkage, known as macrosynteny, is seen between bilaterian phyla divergent Chordata, Echinodermata, Mollusca, and Nemertea. Here, we report a unique pattern genome evolution in Bryozoa, an understudied phylum colonial invertebrates. Using comparative genomics, reconstruct chromosomal history five bryozoans. Multiple ancient fusions followed by mixing led to near-complete loss linkage groups ancestor extant A second wave rearrangements, including fission, then occurred independently two bryozoan classes, further scrambling genomes. We also discover at least derived fusion events shared bryozoans brachiopods, supporting traditional but highly debated Lophophorata hypothesis. Finally, show that fission processes partitioning from Hox clusters onto multiple chromosomes. Our findings demonstrate canonical structure has been lost across all studied representatives entire phylum; reveal group can occur very frequently specific lineages; provide powerful source phylogenetic information.
Language: Английский
Citations
6
PLoS Biology, Journal Year: 2024, Volume and Issue: 22(6), P. e3002661 - e3002661
Published: June 3, 2024
Deuterostomes are a monophyletic group of animals that includes Hemichordata, Echinodermata (together called Ambulacraria), and Chordata. The diversity deuterostome body plans has made it challenging to reconstruct their ancestral condition decipher the genetic changes drove diversification lineages. Here, we generate chromosome-level genome assemblies 2 hemichordate species, Ptychodera flava Schizocardium californicum , use comparative genomic approaches infer chromosomal architecture common ancestor delineate lineage-specific modifications. We show chromosomes (1 N = 23) exhibit remarkable chromosome-scale macrosynteny when compared other deuterostomes can be derived from 24 linkage groups (ALGs). These ALGs in turn match previously inferred bilaterian ALGs, consistent with relatively short transition last origin deuterostomes. Based on this ALG complement, deduced rearrangement events occurred different For example, fusion-with-mixing event produced an Ambulacraria-specific subsequently split into extant hemichordates, while homologous further fused another chromosome sea urchins. Orthologous genes distributed these rearranged enriched for functions various developmental processes. found deeply conserved Hox clusters located highly maintenance likely due lower densities transposable elements within clusters. also provide evidence deuterostome-specific pharyngeal gene cluster was established via combination 3 pre-assembled microsyntenic blocks. suggest since formation new may change regulatory controls genes, have contributed evolution diverse among
Language: Английский
Citations
6
Nature Ecology & Evolution, Journal Year: 2024, Volume and Issue: 8(8), P. 1505 - 1521
Published: July 19, 2024
Species within nearly all extant animal lineages are capable of regenerating body parts. However, it remains unclear whether the gene expression programme controlling regeneration is evolutionarily conserved. Brittle stars a species-rich class echinoderms with outstanding regenerative abilities, but investigations into genetic bases in this group have been hindered by limited genomic resources. Here we report chromosome-scale genome assembly for brittle star Amphiura filiformis. We show that most rearranged among sequenced so far, featuring reorganized Hox cluster reminiscent rearrangements observed sea urchins. In addition, performed an extensive profiling during adult arm and identified sequential waves governing wound healing, proliferation differentiation. conducted comparative transcriptomic analyses other invertebrate vertebrate models appendage uncovered hundreds genes conserved dynamics, particularly proliferative phase regeneration. Our findings emphasize crucial importance to detect long-range conservation between vertebrates classical model systems.
Language: Английский
Citations
6
Genome Research, Journal Year: 2025, Volume and Issue: 35(1), P. 78 - 92
Published: Jan. 1, 2025
Groups of orthologous genes are commonly found together on the same chromosome over vast evolutionary distances. This extensive physical gene linkage, known as macrosynteny, is seen between bilaterian phyla divergent Chordata, Echinodermata, Mollusca, and Nemertea. Here, we report a unique pattern genome evolution in Bryozoa, an understudied phylum colonial invertebrates. Using comparative genomics, reconstruct chromosomal history five bryozoans. Multiple ancient fusions followed by mixing led to near-complete loss linkage groups ancestor extant A second wave rearrangements, including fission, then occurred independently two bryozoan classes, further scrambling genomes. We also discover at least derived fusion events shared bryozoans brachiopods, supporting traditional but highly debated Lophophorata hypothesis suggesting macrosynteny be potentially powerful source phylogenetic information. Finally, show that rearrangements dispersion from Hox clusters onto multiple chromosomes. Our findings demonstrate canonical structure has been lost across all studied representatives entire phylum, reveal group fission can occur very frequently specific lineages.
Language: Английский
Citations
0
eLife, Journal Year: 2024, Volume and Issue: 12
Published: April 4, 2024
Biomineralization had apparently evolved independently in different phyla, using distinct minerals, organic scaffolds, and gene regulatory networks (GRNs). However, diverse eukaryotes from unicellular organisms, through echinoderms to vertebrates, use the actomyosin network during biomineralization. Specifically, remodeling protein, Rho-associated coiled-coil kinase (ROCK) regulates cell differentiation expression vertebrates’ biomineralizing cells, yet, little is known on ROCK’s role invertebrates’ Here, we reveal that ROCK controls formation, growth, morphology of calcite spicules sea urchin larva. elevated skeletogenic cells downstream Vascular Endothelial Growth Factor (VEGF) signaling. inhibition leads skeletal loss disrupts expression. after spicule formation reduces elongation rate induces ectopic branching. Similar phenotypes are observed when inhibited a culture, indicating these due activity specifically cells. Reduced growth enhanced branching also under direct perturbations network. We propose machinery were employed independently, GRNs, regulate biomineral Eukaryotes.
Language: Английский
Citations
3
EvoDevo, Journal Year: 2024, Volume and Issue: 15(1)
Published: Feb. 17, 2024
A challenge for evolutionary developmental (evo-devo) biology is to expand the breadth of research organisms used investigate how animal diversity has evolved through changes in embryonic development. New experimental systems should couple a relevant phylogenetic position with available molecular tools and genomic resources. As phylum sister group chordates, echinoderms extensively contributed our knowledge patterning, organ development cell-type evolution. Echinoderms display variety larval forms diverse shapes, making them suitable compare evolution strategies. However, because laboratory accessibility already techniques, most studies focus on sea urchins stars mainly. comparative approach, field would benefit from including information other members this group, like cucumbers (holothuroids), which little known basis their Here, we review spawning culture methods, morphological information, current state transcriptomic resources cucumbers. With goal system accessible broader community, discuss cucumber embryos larvae can be powerful address open questions evo-devo, understanding origins bilaterian structures.
Language: Английский
Citations
2
Gigabyte, Journal Year: 2024, Volume and Issue: 2024, P. 1 - 13
Published: April 25, 2024
The long-spined sea urchin Diadema setosum is an algal and coral feeder widely distributed in the Indo-Pacific that can cause severe bioerosion on reef community. However, lack of genomic information has hindered study its ecology evolution. Here, we report chromosomal-level genome (885.8 Mb) D. using a combination PacBio long-read sequencing Omni-C scaffolding technology. assembled contains scaffold N50 length 38.3 Mb, 98.1% complete BUSCO (Geno, metazoa_odb10) genes (the single copy score 97.8% duplication 0.3%), 98.6% sequences are anchored to 22 pseudo-molecules/chromosomes. A total 27,478 gene models have were annotated, reaching 28,414 transcripts, including 5,384 tRNA 23,030 protein-coding genes. high-quality presented here valuable resource for ecological evolutionary studies this reef-associated urchin.
Language: Английский
Citations
2
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: May 18, 2024
Abstract The organization of genomes into chromosomes is critical for processes such as genetic recombination, environmental adaptation, and speciation. All animals with bilateral symmetry inherited a genome structure from their last common ancestor that has been highly conserved in some taxa but seemingly unconstrained others. However, the evolutionary forces driving these differences by which they emerge have remained largely uncharacterized. Here we analyze across phylum Annelida using 23 chromosome-level annelid genomes. We find while most annelids maintained bilaterian structure, group containing leeches earthworms possesses completely scrambled develop rearrangement index to quantify extent evolution show rearranged any currently sampled bilaterian. further can be classified two distinct categories—high low rearrangement—largely influenced presence or absence, respectively, chromosome fission events. Our findings demonstrate animal variable within reveal occur both gradual, stepwise fashion rapid, all-encompassing changes over short timescales.
Language: Английский
Citations
2
DNA Research, Journal Year: 2024, Volume and Issue: 31(4)
Published: June 22, 2024
The black sea urchin (Arbacia lixula) is a keystone species inhabiting the coastal shallow waters of Mediterranean Sea, which key driver littoral communities' structure. Here, we present first genome assembly and annotation this species, standing as Arbacioida genome, including both nuclear mitochondrial genomes. To obtain chromosome-level assembly, used combination PacBio high fidelity (HiFi) reads chromatin capture (Omni-C). In addition, generated high-quality coding non-coding genes, by using published RNA-Seq data from several individuals A. lixula gene models closely related species. has total span 607.91 Mb, being consistent with its experimentally estimated size. contains 22 chromosome-scale scaffolds (96.52% length), coincides known karyotype. A 72,767 transcripts were predicted 24,171 coding, 48,596 that included lncRNA, snoRNA, tRNAs. circularized had 15,740 bp comprising 13 protein-coding 2 rRNA, tRNA. This reference will enhance ongoing studies benefit wider scientific community.
Language: Английский
Citations
2