Comparative analysis of the Mercenaria mercenaria genome provides insights into the diversity of transposable elements and immune molecules in bivalve mollusks

Abstract

Background: The hard clam Mercenaria mercenaria is a major marine resource along the Atlantic coasts of North America and has been introduced to other continents for resource restoration or aquaculture activities. Significant mortality events have been reported in the species throughout its native range as a result of diseases (microbial infections, leukemia) and acute environmental stress. In this context, the characterization of the hard clam genome can provide highly needed resources to enable basic (e.g., oncogenesis and cancer transmission, adaptation biology) and applied (clam stock enhancement, genomic selection) sciences.

Results: Using a combination of long and short-read sequencing technologies, a 1.86 Gb chromosome-level assembly of the clam genome was generated. The assembly was scaffolded into 19 chromosomes, with an N50 of 83 Mb. Genome annotation yielded 34,728 predicted protein-coding genes, markedly more than the few other members of the Venerida sequenced so far, with coding regions representing only 2% of the assembly. Indeed, more than half of the genome is composed of repeated elements, including transposable elements. Major chromosome rearrangements were detected between this assembly and another recent assembly derived from a genetically segregated clam stock. Comparative analysis of the clam genome allowed the identification of a marked diversification in immune-related proteins, particularly extensive tandem duplications and expansions in tumor necrosis factors (TNFs) and C1q domain-containing proteins, some of which were previously shown to play a role in clam interactions with infectious microbes. The study also generated a comparative repertoire highlighting the diversity and, in some instances, the specificity of LTR-retrotransposons elements, particularly Steamer elements in bivalves.

Conclusions: The diversity of immune molecules in M. mercenaria may allow this species to cope with varying and complex microbial and environmental landscapes. The repertoire of transposable elements identified in this study, particularly Steamer elements, should be a prime target for the investigation of cancer cell development and transmission among bivalve mollusks.

Keywords: Gene duplication; Genome; Hard clam; Repeats; Steamer elements.

Fig. 1

Contact map of the Mercenaria mercenaria genome assembly. Map generated from Hi-C data showing sequences interaction points in chromosomes (red dots). The color bar indicates the density of contact. The associated karyotype (from Wang and Guo, 2007 [26]) is shown under the plot

Fig. 2

Dotplot contrasting the chromosomes from the two Mercenaria mercenaria genome assemblies. All x-axis represents the nucleotides number (in Mb) of M. mercenaria chromosomes (generated in this study) and all y-axis represents the nucleotides of YKG chromosomes [24]. A red point represents a forward match and a blue point a reverse match

Fig. 3

Phylogenetic tree of Mollusca species. Tree of Mollusca species considered in this study based on single copy gene clusters (14 OGs). The tree scale is 0.1 and the bootstrap is represented at each node

Fig. 4

Phylogenetic tree of TNF domains. TNF domains from all identified genes were extracted and used to generate a multiple alignment and a tree using MAFFT. The tree was drawn using iTOL. Colored branches represent the different orthogroups (the colors correspond to those of Table S8. Label colors also represent OG but highlighting only genes belonging to our Mercenaria mercenaria assembly

Fig. 5

C1qDC proteins in Mercenaria mercenaria. Schematic structural domain representation of putative C1qDC proteins from M. mercenaria

Fig. 6

Phylogenetic relationships of Steamer retrotransposons and their close groups. This tree is based on Neighbor-Joining analysis [33] of RT/RNaseH domain amino acid sequences. Node statistical support values come from non-parametric bootstrapping using 100 replicates and only those > 75% are shown. The three C-clade branches are indicated in color. Sequences from Lottia gigantea (LG), Pinctada fucata (PF) and Crassostrea gigas (CG) are included as known references of C9 groups [32], and SURL elements included as outgroup. Sequences obtained from TBLASTN searches are labelled by their accession number. For Steamer elements members of different taxa are color coded as shown. Givri: Gigantidas vrijenhoeki; Bapla: Bathymodiolus platifrons; Mygal: Mytilus galloprovincialis; Mycor: Mytilus coruscus; Mophi: Modiolus philippinarum; Lifor: Limnoperna fortunei; Myedu: Mytilus edulis; Anbro: Anadara broughtonii; Memer: Mercenaria mercenaria; Drros: Dreissena rostriformis; Cysin: Cyclina sinensis; Ruphi: Ruditapes philippinarum; Pemax: Pecten maximus; Cravi: Crassostrea virginica; Cragi: Crassostrea gigas; Saglo: Saccostrea glomerata