A chromosome-scale genome assembly and karyotype of the ctenophore <i>Hormiphora californensis</i>

Schultz, Darrin T.; Francis, Warren R.; McBroome, Jakob; Christianson, Lynne M.; Haddock, Steven H. D.; Green, Edward

doi:10.1093/g3journal/jkab302

Cited by 28 publications

(24 citation statements)

References 72 publications

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“…INXB, INXC, and INXD are adjacent on chromosome 10 of the chromosome-level assembly of the recently sequenced genome of H. californensis ( Schultz et al 2021 ). There are 226 genes between INXA and the INXB-D cluster in H. californensis .…”

Section: Resultsmentioning

confidence: 99%

“…There are 226 genes between INXA and the INXB-D cluster in H. californensis . Microsynteny is rare between H. californensis and M. leidyi with the largest identifiable blocks of gene microsynteny including only four genes ( Schultz et al 2021 ), but the block that includes INXB, INXC, and INXD is conserved and also includes a fourth gene (ML259910a in M. leidyi and Hcv1.av93.c10.g249.i1 in H. californensis ), which is similar to the FAM166B gene in humans. Interestingly, INXN (Hcv1.av93.c10.g18.i1), which was lost in M. leidyi , is next to INXA in H. californensis and INXG (Hcv1.av93.c10.g192.i1) is situated in between these two sets of innexins (173 genes downstream from INXA and 54 genes upstream of INXB) suggesting the cluster was once more extensive.…”

Section: Resultsmentioning

confidence: 99%

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Independent Innexin Radiation Shaped Signaling in Ctenophores

Ortiz

Bobkov

DeBiasse

et al. 2023

Molecular Biology and Evolution

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Innexins facilitate cell-cell communication by forming gap junctions or non-junctional hemichannels, which play important roles in metabolic, chemical, ionic, and electrical coupling. The lack of knowledge regarding the evolution and role of these channels in ctenophores (comb jellies), the likely sister group to the rest of animals, represents a substantial gap in our understanding of the evolution of intercellular communication in animals. Here we identify and phylogenetically characterize the complete set of innexins of four ctenophores: Mnemiopsis leidyi, Hormiphora californensis, Pleurobrachia bachei, and Beroe ovata. Our phylogenetic analyses suggest that ctenophore innexins diversified independently from those of other animals and were established early in the emergence of ctenophores. We identified a four-innexin genomic cluster, which was present in the last common ancestor of these four species and has been largely maintained in these lineages. Evidence from correlated spatial and temporal gene expression of the M. leidyi innexin cluster suggest that this cluster has been maintained due to constraints related to gene regulation. We describe basic electrophysiological properties of putative ctenophore hemichannels from muscle cells using intracellular recording techniques, showing substantial overlap with the properties of bilaterian innexin channels. Together, our results suggest that the last common ancestor of animals had gap junctional channels also capable of forming functional innexin hemichannels, and that innexin genes have independently evolved in major lineages throughout Metazoa.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Independent Innexin Radiation Shaped Signaling in Ctenophores

Ortiz

Bobkov

DeBiasse

et al. 2023

Molecular Biology and Evolution

View full text Add to dashboard Cite

show abstract

“…INXB, INXC, and INXD are adjacent on chromosome 10 of the chromosome-level assembly of the recently sequenced genome of Hormiphora californensis (Schultz et al 2021). There are 226 genes between INXA and the INXB-D cluster in H. californensis .…”

Section: Resultsmentioning

confidence: 99%

Independent innexin radiation shaped signaling in ctenophores

Ortiz

Bobkov

DeBiasse

et al. 2022

Preprint

View full text Add to dashboard Cite

Innexins facilitate cell-cell communication by forming gap junctions or non-junctional hemichannels, which play important roles in metabolic, chemical, ionic, and electrical coupling. The lack of knowledge regarding the evolution and role of these channels in ctenophores (comb jellies), the likely sister group to the rest of animals, represents a substantial gap in our understanding of the evolution of intercellular communication in animals. Here we identify and phylogenetically characterize the complete set of innexins of four ctenophores:Mnemiopsis leidyi,Hormiphora californensis,Pleurobrachia bachei, andBeroe ovata. Our phylogenetic analyses suggest that ctenophore innexins diversified independently from those of other animals and were established early in the emergence of ctenophores. We identified a four-innexin genomic cluster, which was present in the last common ancestor of these four species and has been largely maintained in these lineages. Evidence from correlated spatial and temporal gene expression of theM. leidyiinnexin cluster suggest that this cluster has been maintained due to constraints related to gene regulation. We describe basic electrophysiological properties of putative ctenophore hemichannels from muscle cells using intracellular recording techniques, showing substantial overlap with the properties of bilaterian innexin channels. Together, our results suggest that the last common ancestor of animals had gap junctional channels also capable of forming functional innexin hemichannels, and that innexin genes have independently evolved in major lineages throughout Metazoa.

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“…For example, the genome of Ephydatia muelleri, not available at the time we assembled our data set in 2018, is dispersed over 1419 scaffolds, even though about 84% of it was contained in the 24 largest scaffolds, encompassing 22 of the 23 chromosomes (Kenny et al, 2020). Virtually complete chromosome scale genome assemblies of non-bilaterians are only now starting to appear, i.e., the ctenophore Hormiphora californensis, where 99.47% of the genome are contained in 13 scaffolds (Schultz et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

“…Virtually complete chromosome scale genome assemblies of non-bilaterians are only now starting to appear, i.e., the ctenophore Hormiphora californensis, where 99.47% of the genome are contained in 13 scaffolds [55].…”

Section: Discussionmentioning

confidence: 99%

Exploring genome gene content and morphological analysis to test recalcitrant nodes in the animal phylogeny

Juravel

Porras

Höhna

et al. 2021

Preprint

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An accurate phylogeny of animals is needed to clarify their evolution, ecology, and impact on shaping the biosphere. Although multi-gene alignments of up to several hundred thousand amino acids are nowadays routinely used to test hypotheses of animal relationships, some nodes towards the root of the animal phylogeny are proving hard to resolve. While the relationships of the non-bilaterian lineages, primarily sponges (Porifera) and comb jellies (Ctenophora), have received much attention since more than a decade, controversies about the phylogenetic position of the worm-like bilaterian lineage Xenacoelomorpha and the monophyly of the “Superphylum” Deuterostomia have more recently emerged. Here we independently analyse novel genome gene content and morphological datasets to assess patterns of phylogenetic congruence with previous amino-acid derived phylogenetic hypotheses. Using statistical hypothesis testing, we show that both our datasets very strongly support sponges as the sister group of all the other animals, Xenoacoelomorpha as the sister group of the other Bilateria, and largely support monophyletic Deuterostomia. Based on these results, we conclude that the last common animal ancestor may have been a simple, filter-feeding organism without a nervous system and muscles, while the last common ancestor of Bilateria might have been a small, acoelomate-like worm without a through gut.

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A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis

Cited by 28 publications

References 72 publications

Independent Innexin Radiation Shaped Signaling in Ctenophores

Independent Innexin Radiation Shaped Signaling in Ctenophores

Independent innexin radiation shaped signaling in ctenophores

Exploring genome gene content and morphological analysis to test recalcitrant nodes in the animal phylogeny

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