Ctenoides ales genome assembly

Title: Chromosome-level genome assembly of the disco clam, Ctenoides ales, a first for the bivalve order LimidaAbstract: 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 datasetCale_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)

标题：迪斯科蛤（Ctenoides ales）的染色体级基因组组装：双壳纲锉蛤目（Limida）的首次报道
摘要：翼形亚纲（Pteriomorphia）包含扇贝、牡蛎、贻贝和魁蚶等具有重要经济价值的类群，其生态、形态与行为多样性极高。该类群演化出五种形态迥异的眼型，为探究新性状演化的分子基础提供了绝佳研究体系。在翼形亚纲双壳类中，锉蛤目（Limida）是唯一缺乏基因组资源的类群，这极大限制了与眼及光转导（phototransduction）相关的系统基因组学分析。本研究首次报道锉蛤类的基因组组装——迪斯科蛤（Ctenoides ales），该物种具有内陷眼、超长触手与闪光行为等特征。本基因组组装采用PacBio长读长测序数据与Dovetail Omni-CTM邻近连接测序技术构建完成。最终组装序列总长约2.3Gb，超过99%的组装序列被锚定至18个假分子支架（pseudomolecule scaffolds）。本研究共注释得到41064个蛋白质编码基因，基于动物界BUSCO（metazoa_obd10）数据库评估的基因组完整度为91.9%。此外，本研究还首次报道了锉蛤目完整注释的线粒体基因组（mitogenome）：该线粒体基因组总长约20Kb，包含12个蛋白质编码基因、22个转运RNA（tRNA）基因、2个核糖体RNA（rRNA）基因，以及一段长度为1589bp的包含复制起始位点的重复序列。迪斯科蛤的核基因组规模显著大于其他翼形亚纲类群，这一差异主要由转座元件序列扩张导致。本研究对基因组中的视蛋白（opsins）——启动光转导过程的信号蛋白——进行了系统排查，结果发现，与亲缘关系最近的带眼类群扇贝不同，迪斯科蛤缺乏通常用于无脊椎动物视觉的横纹肌型Gq蛋白偶联视蛋白的复制事件。事实上，相较于其他翼形亚纲类群（所有类群均存在新近发现的视蛋白亚家族——异视蛋白（xenopsins）的特异性扩张），迪斯科蛤的视蛋白基因数量异常稀少。本染色体级基因组组装与线粒体基因组将为双壳类的比较基因组学与系统发育学研究提供宝贵资源，尤其有助于推动研究不足但极具魅力的锉蛤类群的相关研究。
数据集文件列表：
Cale_mtGenome.fasta：迪斯科蛤（Ctenoides ales）线粒体基因组组装序列
Cale_mtGenome_annotation.bed：迪斯科蛤线粒体基因组注释文件
CollapsedCalesMikado.proteins.fasta.gz：迪斯科蛤基因组注释得到的蛋白质序列文件
CollapsedCalesMikado.transcripts.fasta.gz：迪斯科蛤基因组注释得到的转录本序列文件
SortedFunctionalAnnotationCales.gff3.gz：迪斯科蛤基因组组装的功能注释文件
SoftmaskedCalesGenomeCleanScaffolds.fasta.gz：迪斯科蛤基因组组装的软屏蔽序列文件
Opsin_seqs.aa.fa：迪斯科蛤与其他翼形亚纲双壳类的视蛋白氨基酸序列文件
Opsin_seqs.aln.aa.fa：迪斯科蛤与其他翼形亚纲双壳类的比对后视蛋白氨基酸序列文件
Opsin_treefile.nwk：翼形亚纲视蛋白与外类群序列的最大似然法系统发育树文件（Newick格式）
Opsin_treefile.nxs：翼形亚纲视蛋白与外类群序列的最大似然法系统发育树文件（Nexus格式，已生根）
Opsin_IQTREE.log.txt：视蛋白序列的IQ-TREE2分析日志文件
partition_models.nex.treefile.rooted.nxs：基于1156个单拷贝同源基因的分区分析得到的翼形亚纲双壳类与外类群的最大似然法物种树文件（Nexus格式，已生根）
IQtree2_partition_bivalve.nwk：基于1156个单拷贝同源基因的分区分析得到的翼形亚纲双壳类与外类群的最大似然法物种树文件（Newick格式）