A deep dive into genome assemblies of non-vertebrate animals

Guiglielmoni, Nadège; Rivera‐Vicéns, Ramón E.; Koszul, Romain; Flot, Jean-François

doi:10.24072/pcjournal.128

Cited by 5 publications

(7 citation statements)

References 278 publications

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“…We identified homologues of each of the known sperm motility pathway proteins—GC-A, the potassium-selective CNGK, HCN, CatSper α 1–4, and sNHE—expressed in the adult proteome of A. poculata . Given the presence of the sperm-specific CatSper and sNHE proteins in a proteome generated from whole adult tissue from several animals, it is likely that one or more colonies contained developing spermatocytes [32]. Thus, we suggest that the entire sperm motility pathway operating in sea urchins and M. capitata is also present in A. poculata , indicating a high level of conservation across species with divergent sexual systems, as well as across phyla.…”

Section: Discussionmentioning

confidence: 94%

Section: Methodsmentioning

confidence: 99%

“…A preliminary A. poculata proteome produced by Guiglielmoni [32] using whole adult tissue was queried for expression of PKA C α . Specifically, a custom protein basic local alignment search tool (BLASTp) database was created from a FASTA file containing the A. poculata proteome [32]. Searching the database using the epitope against which the commercial PKA C α antibody was designed (KKGAKNDIIKAFLTEAK) yielded two highly similar protein results, which were confirmed to be isoforms of PKA C α via alignment of their amino acid sequences against human PKA C α with Clustal Omega [33].…”

Section: Methodsmentioning

confidence: 99%

“…The proteome of A. poculata [32] was investigated via local BLASTp for the presence of homologues to proteins making up the canonical sperm motility pathway in other marine invertebrate species, including sea urchins and the coral Montipora capitata [24]. These proteins are GC-A, the potassium-selective CNGK, the hyperpolarization-activated, cyclic nucleotide-gated channel (HCN), the four subunits of CatSper and the sperm-specific Na + /H + exchanger (sNHE).…”

Section: Methodsmentioning

confidence: 99%

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Characterization of a sperm motility signalling pathway in a gonochoric coral suggests conservation across cnidarian sexual systems

Glass,

Ashey,

Okongwu

et al. 2023

Proc. R. Soc. B.

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Most stony corals liberate their gametes into the water column via broadcast spawning, where fertilization hinges upon the activation of directional sperm motility. Sperm from gonochoric and hermaphroditic corals display distinct morphological and molecular phenotypes, yet it is unknown whether the signalling pathways controlling sperm motility are also distinct between these sexual systems. Here, we addressed this knowledge gap using the gonochoric, broadcast spawning coral Astrangia poculata . We found that cytosolic alkalinization of sperm activates the pH-sensing enzyme soluble adenylyl cyclase (sAC), which is required for motility. Additionally, we demonstrate for the first time in any cnidarian that sAC activity leads to protein kinase A (PKA) activation, and that PKA activity contributes to sperm motility activation. Ultrastructures of A. poculata sperm displayed morphological homology with other gonochoric cnidarians, and sAC exhibited broad structural and functional conservation across this phylum. These results indicate a conserved role for pH-dependent sAC-cAMP-PKA signalling in sperm motility across coral sexual systems, and suggest that the role of this pathway in sperm motility may be ancestral in metazoans. Finally, the dynamics of this pH-sensitive pathway may play a critical role in determining the sensitivity of marine invertebrate reproduction to anthropogenic ocean acidification.

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Section: Discussionmentioning

confidence: 94%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Characterization of a sperm motility signalling pathway in a gonochoric coral suggests conservation across cnidarian sexual systems

Glass,

Ashey,

Okongwu

et al. 2023

Proc. R. Soc. B.

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“…With the new genome assembly, we were able to input 99.28 % of the genome to the analysis-only excluding ten unplaced scaffolds. The new assembly has a BUSCO (diptera_odb10) completeness of 99.28 % (Table 1) demonstrating the advantage of long-read sequencing coupled with Hi-C scaffolding (Guiglielmoni et al 2022). Our results indicate the importance of high-quality genomes as the time range of demographic events was shifted significantly in the new inference (Figure 2A-B).…”

Section: Discussionmentioning

confidence: 99%

The interplay of recombination landscape, a transposable element and population history in European populations ofChironomus riparius

Pettrich,

King,

Field

et al. 2024

Preprint

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Genome resolution is often constrained for non-model species. This can be challenging for population genomic studies as estimations are highly dependent on the quality of the reference genome. This is the case for population history inferences where accuracy relies on the correct detection of single-nucleotide polymorphisms (SNPs) and accurate recombination rates. Here, we utilize a novel long-read genome assembly ofChironomus ripariuswith high resolution at a chromosome-scale and reanalyse Illumina resequencing data of five European populations. With the model MSMC2, new population demographies were inferred and compared to an older study based on a fragmented genome. Assembly contiguity and completeness led to an increase in accuracy of past demography, suggesting the onset of divergence of an ancestral population between late Pleistocene and early Holocene. These estimates are additionally supported by paleotemperature data, which reveal significant climate shifts in Central Europe during these times. Recombination severely influences population history estimates. With the new reference genome, it was possible to resolve the recombination landscape on the genome-wide scale across different populations using the tool iSMC. Recombination and the dispersal of transposable elements (TEs) in the genome are suspected to influence each other. One TE, known asCla-element, is suspected to be involved in the divergence of the differentC. ripariuspopulations. As it seems to be highly dynamic in the genome, its potential impact on the recombination landscape was explored. No global pattern could be detected which demonstrated a higher resistance of the recombination landscape to the impact of repetitive elements on genome integrity.

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The Genomics in Emerging Marine Systems Checklist for Clear and Reproducible Genomics in Emerging, Marine Systems

Varney

2023

Integrative and Comparative Biology

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Genome sequencing becomes more accessible and powerful every year, but there is a lack of consensus on what information should be provided in publications that include genomic data. The result is a flood of sequencing data without a framework to evaluate its quality and completeness, hindering reproducibility. In non-model taxa in marine systems, a lack of detail in methods sections often hinders future researchers from adopting improved techniques, leaving them to repeat costly protocols and take up computational (wall) time with programs that are already known to fail. Here, I present a set of guidelines tailored for marine taxa (emerging model organisms) to promote consistency between publications, increase transparency of sequencing projects, and preserve the value of sequence data as sequencing technologies advance. Included is a checklist to 1) guide authors toward including more detailed information in their manuscripts, 2) expand data availability, and 3) assist reviewers to thoroughly vet methods and results of future ‘omic publications. This set of guidelines will support the usefulness of ‘omic data in future analyses by providing a framework to document and evaluate these data, leading to transparent and reproducible genomics research on emerging marine systems.

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A deep dive into genome assemblies of non-vertebrate animals

Cited by 5 publications

References 278 publications

Characterization of a sperm motility signalling pathway in a gonochoric coral suggests conservation across cnidarian sexual systems

Characterization of a sperm motility signalling pathway in a gonochoric coral suggests conservation across cnidarian sexual systems

The interplay of recombination landscape, a transposable element and population history in European populations ofChironomus riparius

The Genomics in Emerging Marine Systems Checklist for Clear and Reproducible Genomics in Emerging, Marine Systems

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