Ctenoides ales genome assembly

Title: Chromosome-level genome assembly of the disco clam, Ctenoides ales, a first for the bivalve order Limida
Abstract: The bivalve subclass Pteriomorphia, which includes the economically important scallops, oysters, mussels, and ark clams, exhibits extreme ecological, morphological, and behavioral diversity. Among this diversity are five morphologically distinct eye types, making Pteriomorphia an excellent setting to explore the molecular basis for the evolution of novel traits. Of pteriomorphian bivalves, Limida is the only order lacking genomic resources, greatly limiting the potential phylogenomic analyses related to eyes and phototransduction. Here, we present the first limid genome assembly, the disco clam, Ctenoides ales, which is characterized by invaginated eyes, exceptionally long tentacles, and a flashing light display. This genome assembly was constructed with PacBio long reads and Dovetail Omni-CTM proximity-ligation sequencing. The final assembly is ~2.3Gb and over 99% of the total length is contained in 18 pseudomolecule scaffolds. We annotated 41,064 protein coding genes and report a BUSCO completeness of 91.9% for metazoa_obd10. Additionally, we report a completely annotated mitochondrial genome, also a first for Limida. The ~20Kb mitogenome has 12 protein coding genes, 22 tRNAs, 2 rRNA genes, and a 1,589 bp duplicated sequence containing the origin of replication. The C. ales nuclear genome size is substantially larger than other pteriomorphian genomes, mainly accounted for by transposable element sequences. We inventoried the genome for opsins, the signaling proteins that initiate phototransduction, and found that, unlike its closest eyed-relatives, the scallops, C. ales lacks duplication of the rhabdomeric Gq-protein coupled opsin that is typically used for invertebrate vision. In fact, C. ales has uncharacteristically few opsins relative to the other pteriomorphian families, all of which have unique expansions of xenopsins, a recently discovered opsin subfamily. This chromosome-level assembly, along with the mitogenome, will be valuable resources for comparative genomics and phylogenetics in bivalves and particularly for the understudied but charismatic limids.

Items in dataset
Cale_mtGenome.fasta - Ctenoides ales mitochondrial genome assemblyCale_mtGenome_annotation.bed - Ctenoides ales mitochondrial genome annotationCollapsedCalesMikado.proteins.fasta.gz - proteins from genome annotation of Ctenoides ales genomeCollapsedCalesMikado.transcripts.fasta.gz - transcripts from genome annotation of Ctenoides ales genomeSortedFunctionalAnnotationCales.gff3.gz - annotation files of Ctenoides ales genome assemblySoftmaskedCalesGenomeCleanScaffolds.fasta.gz - Ctenoides ales genome assembly fileOpsin_seqs.aa.fa - opsin sequences (amino acid) from Ctenoides ales and other pteriomorphian bivalve speciesOpsin_seqs.aln.aa.fa - aligned opsin sequences (amino acid) from Ctenoides ales and other pteriomorphian bivalve speciesOpsin_treefile.nwk - ML phylogenetic tree of pteriomorphian opsins and outgroup sequences (newick format)Opsin_treefile.nxs - ML phylogenetic tree of pteriomorphian opsins and outgroup sequences (nexus format, rooted)Opsin_IQTREE.log.txt - log file for IQ-TREE2 analysis of opsin sequencespartition_models.nex.treefile.rooted.nxs - ML species tree of pteriomorphian bivavles and outgroups based on partitioned analysis of 1,156 single copy orthologs (nexus format, rooted)IQtree2_partition_bivalve.nwk - ML species tree of pteriomorphian bivavles and outgroups based on partitioned analysis of 1,156 single copy orthologs (newick format)