Acceleration of genome rearrangement in clitellate annelids

Abstract

Comparisons of multiple metazoan genomes have revealed the existence of ancestral linkage groups (ALGs), genomic scaffolds sharing sets of orthologous genes that have been inherited from ancestral animals for hundreds of millions of years (Simakov et al. 2022; Schultz et al. 2023) These ALGs have persisted across major animal taxa including Cnidaria, Deuterostomia, Ecdysozoa and Spiralia. Notwithstanding this general trend of chromosome-scale conservation, ALGs have been obliterated by extensive genome rearrangements in certain groups, most notably including Clitellata (oligochaetes and leeches), a group of easily overlooked invertebrates that is of tremendous ecological, agricultural and economic importance (Charles 2019; Barrett 2016). To further investigate these rearrangements, we have undertaken a comparison of 12 clitellate genomes (including four newly sequenced species) and 11 outgroup representatives. We show that these rearrangements began at the base of the Clitellata (rather than progressing gradually throughout polychaete annelids), that the inter-chromosomal rearrangements continue in several clitellate lineages and that these events have substantially shaped the evolution of the otherwise highly conserved Hox cluster.

Keywords: Annelida; Chromosome; Clitellata; Genome; Genome Evolution; Hox Genes; Synteny.

Figure 1:. New clitellate genomes and clitellate-annelid relationships.

A. Four newly sequenced cliitellate annelids (dorsal views, anterior is up). Hirudo verbana (HVE, small adult 4.5, cm long). Haemadipsa rjukjuana (HRJ, adult, 2 cm long). Helobdella austinensis (HAU, adult, 1.5 cm long). Perionyx excavatus (PEX, adult, 11 cm long). B. Phylogenetic relationships (Maximum Likelihood tree based on 250 orthologous genes) among the 23 species (2 mollusks; 9 polychaete annelids; and 12 clitellate annelids- 6 oligochaetes and 6 leeches) used in this study (see Materials and Methods for details). Each species is assigned a three letter identifier. Photography credits: H. verbena and H. austinensis by Christopher J. Winchell © 2024. H. rjukjuana and P. excavatus by Sung-Jin Cho © 2024.

Figure 2:. Rapid genome rearrangement in clitellate annelids.

A. Synteny plot showing orthologs (curved vertical lines) on chromosomal scaffolds (horizontal black bars) between pairs of species. Orthologs are colored based on bilaterian-cnidarian-sponge ancestral linkage groups (BCnS ALGs). Orthologs on significantly-related chromosomes are opaque (Fisher’s exact test ≤ 0.05), and orthologs on non-significant chromosome pairs are translucent. All major annelid clades, except the Clitellata, retain the BCnS ALGs that are conserved in other metazoans, including the scallop Pecten maximus. The genomes of extant clitellates show that there have been extensive structural rearrangements in the branch leading to clitellates, and within the clitellates.

Figure 3:. Increased inter-chromosomal rearrangements in clitellate annelids.

All three panels show significantly large linkage groups from species trios, inferred with the program odp_nway_rbh. The colors do not correspond between the panels. A. Ribbon diagram colored by the 29 linkage groups inferred from the clade Hirudinida. B. Ribbon diagram colored by the 44 linkage groups inferred from the clade Crassiclitellata. C. The ribbon diagram showing members of both the Hirudinida, the Lumbricidae, and the Megascolecidae. The synteny plot showing orthologs (curved vertical lines) on chromosomal scaffolds (horizontal black bars). There are not only rearrangements between the deep Hirudinida-Crassiclitellata node, but among more recently diverged species.

Figure 4:. Dispersal of the Hox Cluster, exemplified in selected oligochaetes (orange) and leeches (blue), relative to polychaete (green) and molluscan (black) outgroups.

Numbers refer to Hox-containing genome scaffolds, which are drawn to scale. Hox genes (colored vertical lines on scaffolds) are not to scale. Taxon names: PMA, Pecten maximus; OFU, Owenia fusiformis; PEC, Paraescarpia echinospica; LRU, Lumbricus rubellus; PEX, Perionyx excavatus; HRJ, Haemadipsa rjukjuana.