Ancient gene linkages support ctenophores as sister to other animals

A central question in evolutionary biology is whether sponges or ctenophores (comb jellies) are the sister group to all other animals. These alternative phylogenetic hypotheses imply different scenarios for the evolution of complex neural systems and other animal-specific traits1,2,3,4,5,6. Conventional phylogenetic approaches based on morphological characters and increasingly extensive gene sequence collections have not been able to definitively answer this question7,8,9,10,11. Here we develop chromosome-scale gene linkage, also known as synteny, as a phylogenetic character for resolving this question12. We report new chromosome-scale genomes for a ctenophore and two marine sponges, and for three unicellular relatives of animals (a choanoflagellate, a filasterean amoeba and an ichthyosporean) that serve as outgroups for phylogenetic analysis. We find ancient syntenies that are conserved between animals and their close unicellular relatives. Ctenophores and unicellular eukaryotes share ancestral metazoan patterns, whereas sponges, bilaterians, and cnidarians share derived chromosomal rearrangements. Conserved syntenic characters unite sponges with bilaterians, cnidarians, and placozoans in a monophyletic clade to the exclusion of ctenophores, placing ctenophores as the sister group to all other animals. The patterns of synteny shared by sponges, bilaterians, and cnidarians are the result of rare and irreversible chromosome fusion-and-mixing events that provide robust and unambiguous phylogenetic support for the ctenophore-sister hypothesis. These findings provide a new framework for resolving deep, recalcitrant phylogenetic problems and have implications for our understanding of animal evolution.journal articl

Conserved novel ORFs in the mitochondrial genome of the ctenophore Beroe forskalii

To date, five ctenophore species’ mitochondrial genomes have been sequenced, and each contains open reading frames (ORFs) that if translated have no identifiable orthologs. ORFs with no identifiable orthologs are called unidentified reading frames (URFs). If truly protein-coding, ctenophore mitochondrial URFs represent a little understood path in early-diverging metazoan mitochondrial evolution and metabolism. We sequenced and annotated the mitochondrial genomes of three individuals of the beroid ctenophore Beroe forskalii and found that in addition to sharing the same canonical mitochondrial genes as other ctenophores, the B. forskalii mitochondrial genome contains two URFs. These URFs are conserved among the three individuals but not found in other sequenced species. We developed computational tools called pauvre and cuttlery to determine the likelihood that URFs are protein coding. There is evidence that the two URFs are under negative selection, and a novel Bayesian hypothesis test of trinucleotide frequency shows that the URFs are more similar to known coding genes than noncoding intergenic sequence. Protein structure and function prediction of all ctenophore URFs suggests that they all code for transmembrane transport proteins. These findings, along with the presence of URFs in other sequenced ctenophore mitochondrial genomes, suggest that ctenophores may have uncharacterized transmembrane proteins present in their mitochondria

Insights into the Biodiversity, Behavior, and Bioluminescence of Deep-Sea Organisms Using Molecular and Maritime Technology

Since its founding, the Monterey Bay Aquarium Research Institute (MBARI) has pioneered unique capabilities for accessing the deep ocean and its inhabitants through focused peer relationships between scientists and engineers. This focus has enabled breakthroughs in our understanding of life in the sea, leading to fundamental advances in describing the biology and the ecology of open-ocean and deep-sea animals. David Packard’s founding principle was the application of technological advances to studying the deep ocean, in part because he recognized the critical importance of this habitat in a global context. Among other fields, MBARI’s science has benefited from applying novel methodologies in molecular biology and genetics, imaging systems, and in situ observations. These technologies have allowed MBARI’s bioluminescence and biodiversity laboratory and worldwide collaborators to address centuries-old questions related to the biodiversity, behavior, and bio-optical properties of organisms living in the water column, from the surface into the deep sea. Many of the most interesting of these phenomena are in the midwater domain—the vast region of ocean between the sunlit surface waters and the deep seafloor

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Chromosome-Scale Genomes, Resolving the Sister Phylum to Other Animals, and Novel Bioluminescent Systems.

Understanding how animals evolved from unicellular life requires comprehensive analyses that sample all animal phyla. However, some major outstanding questions in evolutionary biology, such as the evolutionary provenance of neurons, developmental pathways, and animal-specific genes, remain unanswered for one reason: it is unclear whether sponges (phylum Porifera) or ctenophores (phylum Ctenophora) as the sister phylum to all other animals. Here, we resolved this question using a chromosome-scale, whole-genome comparative approach. First, we generated chromosome-scale genomes of ctenophore species, and of three species that are unicellular, and outgroups to the Metazoa. By comparing these genomes to other chromosome-scale animal genomes, we identified groupings of genes that have persisted together on the same chromosomes since the common ancestor of the Filozoa, more than one billion years ago. We track the fate of these linked genes in the genomes of extant species, and find irreversible chromosomal fusions-with-mixing that preclude sponges from being the sister phylum to other animals. Thus, ctenophores must be the sister phylum to other animals.As a parallel effort, we sought to use transcriptomics and genomics to study a trait that is common to many of the marine species that we studied above: bioluminescence. Light-emitting luciferase proteins are a useful tool for visualizing sub-cellular processes in microscopy, and are an interesting case of convergent evolution in over fifty clades. We used transcriptomics, full-length cDNA sequencing, and protein purification techniques to identify a novel luciferase in the polychaete worm Odontosylllis undecimdonta. This luciferase appears to be specific to the genus Odontosyllis, and there is no evidence for homologs in the transcriptomes of other polychaetes. In addition to the polychate luminescence, we also identified luminescence in a species of deep-sea sponge. This finding is significant, as reports of sponge luminescence in the past have been dubious. We used a biochemical approach to identify the luminous small molecule, coelenterazine, that is used in the bioluminescence reaction. A metagenomics sequencing approach revealed that the sponge sample contained little to no bacteria, and therefore the luminescence produced by the sponge was likely endogenous. Future efforts will focus on genome sequencing, and identifying the luciferase, to determine if the luciferase is truly encoded in the sponge genome

conchoecia/beroe_forskalii_mitogenome: 20171226 release

20171226 release of Beroe forskalii mitogenome annotation documents

Bioluminescence in an Undescribed Species of Carnivorous Sponge (Cladorhizidae) From the Deep Sea

International audienceOne dominant ecological trait in the dimly-lit deep-sea is the ability of organisms to emit bioluminescence. Despite its many ecological roles in deep-sea ecosystems, the presence of inherent bioluminescence in marine sponges has been debated for more than a century. This work reports repeated observations of luminescence from six individuals of an undescribed carnivorous sponge species (Cladorhizidae) sampled near 4,000 m depth off Monterey Bay (CA, United States). These are the first fully documented records of bioluminescence in the phylum Porifera. Videos and photographs of the sponges' bioluminescence were recorded on board after collection and in vitro bioluminescence assays indicate that the bioluminescence system is a coelenterazine-based luciferase. Coelenterazine luciferin is already described in various organisms such as cnidarians, chaetognaths, copepods, cephalopods, ctenophores, ostracods, and some mysid or decapod shrimps. Based on these observations we discuss new ecological hypotheses of functional traits such as bioluminescence and carnivory in deep sea organisms

The complete mitochondrial genome of Dascyllus trimaculatus (Rüppell, 1829)

Damselfishes (family Pomacentridae) comprise approximately 400 species that play an important ecological role in temperate and coral reefs. Here, for the first time, we assemble and annotate the mitochondrial genome of Dascyllus trimaculatus, the three-spot dascyllus, a planktivorous damselfish that primarily recruits in anemones. The circular genome of D. trimaculatus is 16,967 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region. Gene arrangement and codon usage is similar to reported mitochondrial genomes of other damselfish genera, and a phylogenetic analysis of a set of damselfish representatives is consistent with known evolutionary analyses

Chromosome-level genome of the three-spot damselfish, Dascyllus trimaculatus

Damselfishes (Family: Pomacentridae) are a group of ecologically important, primarily coral reef fishes that include over 400 species. Damselfishes have been used as model organisms to study recruitment (anemonefishes), the effects of ocean acidification (spiny damselfish), population structure, and speciation (Dascyllus). The genus Dascyllus includes a group of small-bodied species, and a complex of relatively larger bodied species, the Dascyllus trimaculatus species complex that is comprised of several species including D. trimaculatus itself. The three-spot damselfish, D. trimaculatus, is a widespread and common coral reef fish species found across the tropical Indo-Pacific. Here, we present the first-genome assembly of this species. This assembly contains 910 Mb, 90% of the bases are in 24 chromosome-scale scaffolds, and the Benchmarking Universal Single-Copy Orthologs score of the assembly is 97.9%. Our findings confirm previous reports of a karyotype of 2n = 47 in D. trimaculatus in which one parent contributes 24 chromosomes and the other 23. We find evidence that this karyotype is the result of a heterozygous Robertsonian fusion. We also find that the D. trimaculatus chromosomes are each homologous with single chromosomes of the closely related clownfish species, Amphiprion percula. This assembly will be a valuable resource in the population genomics and conservation of Damselfishes, and continued studies of the karyotypic diversity in this clade