The evo‐devo of molluscs: Insights from a genomic perspective

Yang, Zhihui; Zhang, Lingling; Hu, Jiang; Wang, Jing; Bao, Zhenmin; Wang, Shi

doi:10.1111/ede.12336

Cited by 33 publications

(35 citation statements)

References 151 publications

(224 reference statements)

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“…Despite their remarkable biological, evolutionary and ecological significance, molluscs have long been neglected from a genomic perspective ( 7 , 8 ). The rapid development of high-throughput sequencing technologies has pushed molluscan research into the genomics era.…”

Section: Introductionmentioning

confidence: 99%

MolluscDB: an integrated functional and evolutionary genomics database for the hyper-diverse animal phylum Mollusca

Liu

et al. 2020

Nucleic Acids Research

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Mollusca represents the second largest animal phylum but remains poorly explored from a genomic perspective. While the recent increase in genomic resources holds great promise for a deep understanding of molluscan biology and evolution, access and utilization of these resources still pose a challenge. Here, we present the first comprehensive molluscan genomics database, MolluscDB (http://mgbase.qnlm.ac), which compiles and integrates current molluscan genomic/transcriptomic resources and provides convenient tools for multi-level integrative and comparative genomic analyses. MolluscDB enables a systematic view of genomic information from various aspects, such as genome assembly statistics, genome phylogenies, fossil records, gene information, expression profiles, gene families, transcription factors, transposable elements and mitogenome organization information. Moreover, MolluscDB offers valuable customized datasets or resources, such as gene coexpression networks across various developmental stages and adult tissues/organs, core gene repertoires inferred for major molluscan lineages, and macrosynteny analysis for chromosomal evolution. MolluscDB presents an integrative and comprehensive genomics platform that will allow the molluscan community to cope with ever-growing genomic resources and will expedite new scientific discoveries for understanding molluscan biology and evolution.

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Section: Introductionmentioning

confidence: 99%

MolluscDB: an integrated functional and evolutionary genomics database for the hyper-diverse animal phylum Mollusca

Liu

et al. 2020

Nucleic Acids Research

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“…Despite great ecological, economical, and medical importance, stylommatophoran land snails have been underrepresented in whole genome sequencing projects ( Yang et al 2020 ), mainly because of their large repetitive genomes ( C -values between 1.68 and 4.00, see http://www.genomesize.com/ ). Usually, sequencing coverage above 30× is recommended to overcome this problem ( Dominguez Del Angel et al 2018 ), but this is often financially challenging for individual research groups.…”

Section: Introductionmentioning

confidence: 99%

The draft genome sequence of the grove snail Cepaea nemoralis

Saenko

Groenenberg

Davison

2021

G3 Genes|Genomes|Genetics

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Studies on the shell color and banding polymorphism of the grove snail Cepaea nemoralis and the sister taxon Cepaea hortensis have provided compelling evidence for the fundamental role of natural selection in promoting and maintaining intraspecific variation. More recently, Cepaea has been the focus of citizen science projects on shell color evolution in relation to climate change and urbanization. C. nemoralis is particularly useful for studies on the genetics of shell polymorphism and the evolution of “supergenes,” as well as evo-devo studies of shell biomineralization, because it is relatively easily maintained in captivity. However, an absence of genomic resources for C. nemoralis has generally hindered detailed genetic and molecular investigations. We therefore generated ∼23× coverage long-read data for the ∼3.5 Gb genome, and produced a draft assembly composed of 28,537 contigs with the N50 length of 333 kb. Genome completeness, estimated by BUSCO using the metazoa dataset, was 91%. Repetitive regions cover over 77% of the genome. A total of 43,519 protein-coding genes were predicted in the assembled genome, and 97.3% of these were functionally annotated from either sequence homology or protein signature searches. This first assembled and annotated genome sequence for a helicoid snail, a large group that includes edible species, agricultural pests, and parasite hosts, will be a core resource for identifying the loci that determine the shell polymorphism, as well as in a wide range of analyses in evolutionary and developmental biology, and snail biology in general.

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“…Nevertheless, these symbionts have highly reduced genome sizes, having lost ∼60% protein-coding genes (PCGs) that are typically found in free-living thioautotrophs, as well as the endosymbiotic thioautotrophs of sibognilid tubeworms ( Li, Liles, et al. 2018 ; Yang, Sun, et al. 2020 ), bathymodiolin mussels ( Ponnudurai et al.…”

Section: Introductionmentioning

confidence: 99%

Host–Endosymbiont Genome Integration in a Deep-Sea Chemosymbiotic Clam

Sun

et al. 2020

Molecular Biology and Evolution

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Endosymbiosis with chemosynthetic bacteria has enabled many deep-sea invertebrates to thrive at hydrothermal vents and cold seeps, but most previous studies on this mutualism have focused on the bacteria only. Vesicomyid clams dominate global deep-sea chemosynthesis-based ecosystems. They differ from most deep-sea symbiotic animals in passing their symbionts from parent to offspring, enabling intricate co-evolution between the host and the symbiont. Here, we sequenced the genomes of the clam Archivesica marissinica (Bivalvia: Vesicomyidae) and its bacterial symbiont to understand the genomic/metabolic integration behind this symbiosis. At 1.52 gigabases, the clam genome encodes 28 genes horizontally transferred from bacteria, a large number of pseudogenes and transposable elements whose massive expansion corresponded to the timing of the rise and subsequent divergence of symbiont-bearing vesicomyids. The genome exhibits gene family expansion in cellular processes that likely facilitate chemoautotrophy, including gas delivery to support energy and carbon production, metabolite exchange with the symbiont, and regulation of the bacteriocyte population. Contraction in cellulase genes is likely adaptive to the shift from phytoplankton-derived to bacteria-based food. It also shows contraction in bacterial recognition gene familie, indicative of suppressed immune response to the endosymbiont. The gammaproteobacterium endosymbiont has a reduced genome of 1.03 megabases but retains complete pathways for sulfur oxidation, carbon fixation, and biosynthesis of 20 common amino acids, indicating the host’s high dependence on the symbiont for nutrition. Overall, the host-symbiont genomes show not only tight metabolic complementarity, but also distinct signatures of co-evolution allowing the vesicomyids to thrive in chemosynthesis-based ecosystems.

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The evo‐devo of molluscs: Insights from a genomic perspective

Cited by 33 publications

References 151 publications

MolluscDB: an integrated functional and evolutionary genomics database for the hyper-diverse animal phylum Mollusca

MolluscDB: an integrated functional and evolutionary genomics database for the hyper-diverse animal phylum Mollusca

The draft genome sequence of the grove snail Cepaea nemoralis

Host–Endosymbiont Genome Integration in a Deep-Sea Chemosymbiotic Clam

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