Ctenoides ales genome assembly

<b>Title:</b> Chromosome-level genome assembly of the disco clam, <i>Ctenoides ales</i>, a first for the bivalve order Limida<b>Abstract: </b>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, <i>Ctenoides ales</i>, 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-C^TM 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 <i>C. ales</i> 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, <i>C. ales</i> lacks duplication of the rhabdomeric G_q-protein coupled opsin that is typically used for invertebrate vision. In fact, <i>C. ales</i> 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.<br><b>Items in dataset</b>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)<br>

### 标题：闪光蛤（<i>Ctenoides ales</i>）染色体级基因组组装：双壳纲锉蛤目（Limida）的首个基因组资源

摘要：翼形亚纲（Pteriomorphia）是双壳纲中涵盖扇贝、牡蛎、贻贝与毛蚶等经济物种的类群，展现出极高的生态、形态与行为多样性。该类群拥有五种形态迥异的眼型，使其成为探索新性状演化分子机制的理想研究体系。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，极大限制了与眼及光转导相关的系统基因组学研究。本研究报道了首个锉蛤目基因组组装成果——闪光蛤（<i>Ctenoides ales</i>），该物种具有内陷型眼、超长触手与闪光行为特征。本基因组组装基于PacBio长读长测序与Dovetail Omni-C^TM邻近连接测序技术构建完成。最终组装的基因组大小约为2.3Gb，总序列长度的99%以上被锚定至18条假染色体支架中。我们共注释得到41064个蛋白质编码基因，基于metazoa_obd10数据库的BUSCO（Benchmarking Universal Single-Copy Orthologs）完整度为91.9%。此外，本研究还报道了首个锉蛤目完整注释的线粒体基因组。该线粒体基因组大小约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的包含复制起点的重复序列。闪光蛤的核基因组尺寸显著大于其他翼形亚纲类群的基因组，该差异主要由转座因子序列扩张所致。我们对基因组中的视蛋白——启动光转导过程的信号蛋白——进行了系统筛查，结果发现，与亲缘关系最近的眼类类群扇贝不同，闪光蛤缺乏通常用于无脊椎动物视觉的杆体型Gq蛋白偶联视蛋白的复制事件。实际上，相较于其他翼形亚纲类群（这些类群均存在新近发现的视蛋白亚家族xenopsins的独特扩张），闪光蛤的视蛋白基因数量异常稀少。该染色体级基因组组装结果与线粒体基因组将成为双壳类，尤其是研究不足但极具魅力的锉蛤类的比较基因组学与系统发育学研究的宝贵资源。

数据集文件：
1. Cale_mtGenome.fasta：闪光蛤线粒体基因组组装文件
2. Cale_mtGenome_annotation.bed：闪光蛤线粒体基因组注释文件
3. CollapsedCalesMikado.proteins.fasta.gz：闪光蛤基因组注释得到的蛋白质序列文件
4. CollapsedCalesMikado.transcripts.fasta.gz：闪光蛤基因组注释得到的转录本序列文件
5. SortedFunctionalAnnotationCales.gff3.gz：闪光蛤基因组组装的功能注释文件
6. SoftmaskedCalesGenomeCleanScaffolds.fasta.gz：经软屏蔽处理的闪光蛤基因组组装序列文件
7. Opsin_seqs.aa.fa：闪光蛤与其他翼形亚纲双壳类的视蛋白氨基酸序列文件
8. Opsin_seqs.aln.aa.fa：闪光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
9. Opsin_treefile.nwk：翼形亚纲视蛋白与外类群序列的最大似然系统发育树文件（Newick格式）
10. Opsin_treefile.nxs：翼形亚纲视蛋白与外类群序列的最大似然系统发育树文件（Nexus格式，已生根）
11. Opsin_IQTREE.log.txt：视蛋白序列IQ-TREE2分析的日志文件
12. 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物种树文件（Nexus格式，已生根）
13. 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物种树文件（Newick格式）