van Dorssen Monique, Belcher Emily K, Gallegos Cristóbal, Hodgins Kathryn A, Monro Keyne
School of Biological Sciences, Monash University, Victoria, Australia.
J Hered. 2025 Aug 23;116(5):702-712. doi: 10.1093/jhered/esaf025.
Haplotype-resolved (phased) genome assemblies are emerging as important assets for genomic studies of species with high heterozygosity, but remain lacking for key animal lineages. Here, we use PacBio HiFi and Omni-C technologies to assemble the first phased, annotated, chromosome-level genome for any annelid: the reef-building tubeworm Galeolaria caespitosa (Serpulidae). The assembly is 803.5 Mbp long (scaffold N50 = 76.5 Mbp) for haplotype 1 and 789.3 Mbp long (scaffold N50 = 75.4 Mbp) for haplotype 2, which are arranged into 11 pairs of chromosomes showing no sign of sex chromosomes. This compares with cytological analyses reporting 12 to 13 pairs in G. caespitosa's closest relatives, including species that are protandrous hermaphrodites. We combined long-read and short-read transcriptome sequencing to annotate both haplotypes, resulting in 30,495 predicted proteins for haplotype 1, 27,423 proteins for haplotype two, and 79.5% of proteins with at least one functional annotation. We also assembled a mitochondrial genome 23 kbp long, annotating all genes typically found in mitochondrial DNA apart from those coding the 16S ribosomal subunit (rrnL) and the protein atp8-a short, fast-evolving mitochondrial gene missing in other metazoans. Comparing G. caespitosa's genome to those of three other annelids reveals limited collinearity despite 36.0% of shared orthologous gene clusters (4,238 of 11,763 clusters counted in G. caespitosa), suggesting extensive chromosomal rearrangements among lineages. New high-quality annelid genomes may help resolve the genetic and evolutionary basis of this diversity.
单倍型解析（定相）的基因组组装正成为高杂合度物种基因组研究的重要资产，但关键动物谱系仍缺乏此类组装。在此，我们使用PacBio HiFi和Omni-C技术，为任何一种环节动物组装了首个定相、注释、染色体水平的基因组：造礁管虫Galeolaria caespitosa（龙介虫科）。单倍型1的组装长度为803.5 Mbp（支架N50 = 76.5 Mbp），单倍型2的组装长度为789.3 Mbp（支架N50 = 75.4 Mbp），它们被排列成11对染色体，未显示出性染色体的迹象。这与细胞学分析报告的G. caespitosa最亲近的亲属中有12至13对染色体形成对比，这些亲属包括雄性先熟的雌雄同体物种。我们结合长读长和短读长转录组测序对两个单倍型进行注释，单倍型1预测有30,495个蛋白质，单倍型2有27,423个蛋白质，79.5%的蛋白质至少有一个功能注释。我们还组装了一个23 kbp长的线粒体基因组，注释了线粒体DNA中通常发现的所有基因，但编码16S核糖体亚基（rrnL）的基因和蛋白质atp8除外——atp8是一个短的、快速进化的线粒体基因，在其他后生动物中缺失。将G. caespitosa的基因组与其他三种环节动物的基因组进行比较，发现尽管有36.0%的共享直系同源基因簇（在G. caespitosa中统计的11,763个簇中有4,238个），但共线性有限，这表明谱系间存在广泛的染色体重排。新的高质量环节动物基因组可能有助于解析这种多样性的遗传和进化基础。
