Chromosome-level genome of Capitulum mitella reveals an ancient whole-genome duplication event and intertidal adaptation of barnacles

Abstract

Barnacles are the only sessile crustaceans inhabiting intertidal zone, an extremely stressful environment for sessile organisms. Herein, we report the chromosome-level genome of a stalked barnacle, Capitulum mitella, which is a dominant intertidal cirripede of the west Pacific Ocean coast. After comprehensive comparative genomic analyses, it is first time to find an ancient whole-genome duplication (WGD) event that preceded the divergence of Lepadomorpha and Sessilia approximately 237 million years ago. The retained duplicated genes of WGD are primarily enriched in many environmental information processing pathways, shedding lights on its adaptive evolution of intertidal sessile life. In addition, transcriptomic and metabolomic sequencing and analyses of C. mitella indicated that the upregulation of some expanded anti-stress factors and accumulation of acyl-carnitines help barnacles adapt to stressful intertidal conditions. Therefore, this study provides a valuable resource for understanding the unique intertidal adaptation mechanism of sessile crustaceans, and reveals novel WGD events in invertebrates.

Convergent evolution of barnacles and molluscs sheds lights in origin and diversification of calcareous shell and sessile lifestyle

“…Mollusc ALPs were mostly intact but lacked such specific motif of barnacles. This specific motif arose from the ancestral ALPs and thus evolved before the divergence of the two kinds of barnacles (greater than 237 MYA) [22]. Surprisingly, we found that this motif remained highly conserved, and 52 of the 55 amino acid sites were identical (100%) among 35 ALPs of the two barnacles, despite their distant evolutionary divergence.…”

“…The protein-coding genes of nine arthropods and four molluscs were collected from NCBI genome database and used for gene family analysis, including Capitulum mitella (PRJNA753937 [23]), Amphibalanus amphitrite (PRJNA751628) [24], Eulimnadia texana (PRJNA352082) [25], Eurytemora affinis (PRJNA423276) [26], Tigriopus californicus (PRJNA237968) [27], Armadillidium vulgare (PRJNA501402) [28], Parhyale hawaiensis (PRJNA306836) [29], Litopenaeus vannamei (PRJNA438564) [30], Procambarus virginalis (PRJNA356499) [31], Mizuhopecten yessoensis (PRJNA390633) [32], Crassostrea gigas (PRJEB35351) [33], Modiolus philippinarum (PRJNA328544) [34] and Octopus bimaculoides (PRJNA305125) [35]. Gene family clustering was performed on the protein-coding genes of nine arthropods using O rtho F inder .…”

“…Genome data and annotated protein-coding genes of C. mitella have been deposited in NCBI GenBank with the accession number PRJNA753937 and the Dryad Digital Repository () [23]. The protein sequences of expanded shell-formation-related gene families and settlement-related gene families have been deposited in the Dryad Digital Repository () [44].…”

“…3,4-dihydroxyphenylalanine (DOPA) modification of foot proteins has been suggested to play important roles in mollusc settlement [21]. In this study, based on our newly assembled chromosome-level genome of a stalked barnacle [22], we performed thorough comparative genomics analyses with published genomes of molluscs (e.g. oysters and mussels), crustaceans and other relative barnacles.…”

“…In this study, based on our newly assembled chromosome-level genome of a stalked barnacle [22], we performed thorough comparative genomics analyses with published genomes of molluscs (e.g. oysters and mussels), crustaceans and other relative barnacles.…”