A glimpse into mollusk genomics from the de novo genome of Arion vulgaris MoquinTandon, 1855 (Gastropoda, Stylommatophora)

Chen, Zeyuan (2023): A glimpse into mollusk genomics from the de novo genome of Arion vulgaris MoquinTandon, 1855 (Gastropoda, Stylommatophora). Dissertation, LMU München: Fakultät für Biologie

Abstract

Mollusks are among nature’s greatest innovators, representing some of the most ancient and evolutionary successful animals, with a tremendous diversity in morphology, behavior, lifestyle and habitats. Since the beginning of human civilization, this taxon has received a great deal of attention, for example as ornaments, currency, and diet, and is nowadays closely linked to the economy, health and ecology of human society. For more than two centuries, malacologists have laid a solid foundation for our understanding on the evolution of the phylum Mollusca through behavioral and environmental observations, as well as morphological and anatomical studies. The beginning of the era of genetic and genomic reconstruction of natural history has allowed gaining a complementary perspective on molluscan diversity and evolution. A genome contains the complete genetic information of an organism or a cell, passed from one generation to the next. A reference genome, i.e., a representative nucleic acid sequence database of a target species, reveals the structure, organization and functional features of genes, and therefore serves as a foundation for molecular and genomic studies. Recent improvements in sequencing technologies have provided the ability to produce high-quality genome assemblies in a shorter period of time and with affordable costs. However, relative to the huge number of extant species, molluscan genomic resources lag far behind, and are highly uneven across classes and taxa. For example, up to now (August 2022) no sequenced and assembled genomes are available for four out of the eight mollusk classes (Scaphopoda, Solenogastres, Caudofoveata, Monoplacophora). Gastropods account for 80% of extant species in the phylum Mollusca. While the total number of reported gastropod genomes (49) accounts for 45% of published mollusk genomes, this only represents 0.05% of all known gastropod species. During the course of my dissertation, we generated whole-genome and transcriptome data for Arion vulgaris Moquin-Tandon, 1855 (Mollusca: Gastropoda: Stylommatophora), a notorious agricultural pest in Europe and thus an ecologically and economically important species. We assembled a chromosome-level genome of A. vulgaris with considerable completeness and contiguous, annotated genes and repetitive elements, as well as its mitochondrial genome. Using the mitogenome, we explored the mitochondrial evolutionary patterns as well as phylogenetic relationships of stylommatophoran land snails and slugs. Using whole-genome data, we identified single-copy orthologous genes among major gastropod groups, and recovered Psilogastropoda s.l., that is Patellogastropoda as sister to Vetigastropoda and Neomphalina, for deep gastropod phylogeny. As the first reported genome of a land slug, we have also made extensive comparisons between the genome of Arion vulgaris with land snails and other aquatic and marine species of the clade Heterobranchia. We identified genes that are specific/expanded/positively selected in A. vulgaris, which show functional relatedness to its strong adaptive capacities. Furthermore, we showed that the whole-genome duplication event that occurred approximately 93–109 Mya shared by Stylommatophora species might have promoted stylommatophoran land invasion, speciation, and adaptive radiation. Small-scale gene duplication, i.e., a formidable recent expansion of transposable elements of A. vulgaris, might have additionally driven its genetic innovation and quick adaptation, promoting invasion of new areas and success in changing habitats and environments.

• Dokumententyp: Dissertationen (Dissertation, LMU München)
• Keywords: slug, water-land transition, invasive, evolution, transposable elements, whole-genome duplication, adaptation
• Themengebiete: 500 Naturwissenschaften und Mathematik ; 500 Naturwissenschaften und Mathematik > 570 Biowissenschaften, Biologie
• Fakultäten: Fakultät für Biologie
• Sprache der Hochschulschrift: Englisch
• Datum der mündlichen Prüfung: 27. Februar 2023
• 1. Bericht­erstatter:in: Schrödl, Michael