Unraveling the Mysteries of Sleep: Exploring Phylogenomic Sleep Signals in the Recently Characterized Archaeal Phylum Lokiarchaeota near Loki's Castle DOI Creative Commons
Seithikurippu R. Pandi‐Perumal, Konda Mani Saravanan, Sayan Paul

и другие.

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

Опубликована: Ноя. 3, 2024

Abstract Sleep is a universally conserved behavior with an elusive origin and uncertain evolutionary purpose. Leveraging phylogenomics, we investigate the foundations of sleep by identifying orthologs Human sleep-related genes in Lokiarchaeota Asgard superphylum. Our findings indicate suite associated energy metabolism cellular repair, suggesting primordial role maintenance. This data lends credence to idea that improves organismal fitness across time acting as restorative process. Notably, our approach demonstrates phylogenomics more useful than standard phylogenetics for clarifying common traits. By offering insight into history putting forth novel model framework research taxa, these contribute growing understanding molecular foundation sleep. study lays groundwork further investigations importance various organisms, which could have consequences human health deeper comprehension related fundamental processes life. Graphical

Язык: Английский

Annelid Comparative Genomics and the Evolution of Massive Lineage-specific Genome Rearrangement in Bilaterians DOI Creative Commons
Thomas D. Lewin,

Isabel Jiah-Yih Liao,

Yi‐Jyun Luo

и другие.

Molecular Biology and Evolution, Год журнала: 2024, Номер 41(9)

Опубликована: Авг. 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.

Язык: Английский

Процитировано

12

Evolving perspectives in Hymenoptera systematics: Bridging fossils and genomes across time DOI Creative Commons
Y. Miles Zhang, Silas Bossert, Tamara Spasojevic

и другие.

Systematic Entomology, Год журнала: 2024, Номер unknown

Опубликована: Июль 18, 2024

Abstract The recent advances in sequencing technologies, phylogenomics and divergence dating methods call for an integrative review of the current state Hymenoptera systematics. We here explore impact these latest developments on phylogeny our understanding timing evolution, while identifying methodological constraints persistent knowledge gaps that warrant further investigation. Our highlights lack consensus among backbone between key phylogenomic studies, as higher level remains unresolved nodes such relationships Eusymphyta, within Infraorder Proctotrupomorpha placements superfamilies Ichneumonoidea, Ceraphronoidea Vespoidea. Furthermore, we underline huge variation age estimates detect several major and/or disagreements fossil record available estimates, either due to poorly studied or problematic both. To better understand evolution role diversification factors, will need continuous efforts (i) reconcile conflicts morphological molecular phylogenies, by improving taxon sampling underrepresented lineages, applying novel techniques study morphology, making use genome‐scale data critically assessing incongruences genetic markers; (ii) improve record, exercising taxonomy bringing together paleontologists neontologists; (iii) relying tip approaches bridge fossils, morphology genomes across time.

Язык: Английский

Процитировано

8

Unbiased anchors for reliable genome-wide synteny detection DOI Creative Commons

Karl K. Käther,

Andreas Remmel,

Steffen Lemke

и другие.

Algorithms for Molecular Biology, Год журнала: 2025, Номер 20(1)

Опубликована: Апрель 5, 2025

Язык: Английский

Процитировано

1

Exploring the correlation between speciation and genome rearrangements DOI Creative Commons
Javier del Campo

Peer Community In Genomics, Год журнала: 2025, Номер unknown

Опубликована: Май 14, 2025

Язык: Английский

Процитировано

1

​​Fusion, fission, and scrambling of the bilaterian genome in Bryozoa DOI Creative Commons
Thomas D. Lewin,

Isabel Jiah-Yih Liao,

Mu-En Chen

и другие.

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

Опубликована: Фев. 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.

Язык: Английский

Процитировано

6

Molluscan systematics: historical perspectives and the way ahead DOI Open Access
Biyang Xu,

Lingfeng Kong,

Jin Sun

и другие.

Biological reviews/Biological reviews of the Cambridge Philosophical Society, Год журнала: 2024, Номер unknown

Опубликована: Ноя. 6, 2024

ABSTRACT Mollusca, the second‐most diverse animal phylum, is estimated to have over 100,000 living species with great genetic and phenotypic diversity, a rich fossil record, considerable evolutionary significance. Early work on molluscan systematics was grounded in morphological anatomical studies. With transition from oligo gene Sanger sequencing cutting‐edge genomic technologies, molecular data has been increasingly utilised, providing abundant information for reconstructing phylogenetic tree. However, relationships among within most major lineages of Mollusca long contentious, often due limited markers, insufficient taxon sampling conflict. Fortunately, remarkable progress made recent years, which shed light how groups evolved. In this review systematics, we first synthesise current understanding Tree Life at higher taxonomic levels. We then discuss micromolluscs, adult individuals body size smaller than 5 mm, offer unique insights into Mollusca's vast diversity deep phylogeny. Despite advancements, our knowledge phylogeny still needs refinement. Further advancements will arise integrating comprehensive sets, including genome‐scale data, exceptional fossils, digital (including internal structures). Enhanced access these combined increased collaboration morphologists, palaeontologists, developmental biologists, phylogeneticists, significantly advance field.

Язык: Английский

Процитировано

4

Fusion, fission, and scrambling of the bilaterian genome in Bryozoa DOI Creative Commons
Thomas D. Lewin,

Isabel Jiah-Yih Liao,

Mu-En Chen

и другие.

Genome Research, Год журнала: 2025, Номер 35(1), С. 78 - 92

Опубликована: Янв. 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.

Язык: Английский

Процитировано

0

Decontamination of DNA sequences from a Streptomyces genome for optimal genome mining DOI

Raul Vitor Ferreira de Oliveira,

Leandro M. Garrido, Gabriel Padilla

и другие.

Brazilian Journal of Microbiology, Год журнала: 2025, Номер unknown

Опубликована: Янв. 15, 2025

Язык: Английский

Процитировано

0

Comprehensive analysis of 111 Pleuronectiformes mitochondrial genomes: insights into structure, conservation, variation and evolution DOI Creative Commons
Suxu Tan, Wenwen Wang, Jinjiang Li

и другие.

BMC Genomics, Год журнала: 2025, Номер 26(1)

Опубликована: Янв. 20, 2025

Язык: Английский

Процитировано

0

Exploring Genome Architecture as a Source of Phylogenetic Characters for Resolving the Apulmonate Arachnid Polytomy DOI
Benjamin C. Klementz, Siddharth Kulkarni, Kaitlyn M. Abshire

и другие.

Опубликована: Янв. 1, 2025

Язык: Английский

Процитировано

0