Comparative Genomics Reveals Evolutionary Drivers of Sessile Life and Left-right Shell Asymmetry in Bivalves

Appeltans, 2012, The magnitude of global marine species diversity, Curr Biol, 22, 2189, 10.1016/j.cub.2012.09.036 Tibabuzo Perdomo, 2018, Changes in cementation of reef building oysters transitioning from larvae to adults, ACS Appl Mater Interfaces, 10, 14248, 10.1021/acsami.8b01305 Grabowski, 2007, Restoring oyster reefs to recover ecosystem services, Theor Ecol Series, 4, 281, 10.1016/S1875-306X(07)80017-7 Kroeker, 2013, Impacts of ocean acidification on marine organisms: quantifying sensitivities and interaction with warming, Glob Chang Biol, 19, 1884, 10.1111/gcb.12179 Priemel, 2017, Rapid self-assembly of complex biomolecular architectures during mussel byssus biofabrication, Nat Commun, 8, 14539, 10.1038/ncomms14539 Li, 2017, Scallop genome reveals molecular adaptations to semi-sessile life and neurotoxins, Nat Commun, 8, 1721, 10.1038/s41467-017-01927-0 Burkett, 2010, Oysters produce an organic-inorganic adhesive for intertidal reef construction, J Am Chem Soc, 132, 12531, 10.1021/ja104996y Stanley, 1970, Relation of Shell Form to Life Habits of the Bivalvia (Mollusca), Geological Society of America Bulletin, 125, 296 Guo, 1999, Molluscan aquaculture in China, J Shellfish Res, 18, 19 Zhang, 2012, The oyster genome reveals stress adaptation and complexity of shell formation, Nature, 490, 49, 10.1038/nature11413 Wang, 2017, Scallop genome provides insights into evolution of bilaterian karyotype and development, Nat Ecol Evol, 1, 120, 10.1038/s41559-017-0120 Du, 2017, The pearl oyster Pinctada fucata martensii genome and multi-omic analyses provide insights into biomineralization, Gigascience, 6, 1, 10.1093/gigascience/gix059 Simakov, 2013, Insights into bilaterian evolution from three spiralian genomes, Nature, 493, 526, 10.1038/nature11696 Ren, 2010, Unusual conservation of mitochondrial gene order in Crassostrea oysters: evidence for recent speciation in Asia, BMC Evol Biol, 10, 394, 10.1186/1471-2148-10-394 Pimm, 2014, The biodiversity of species and their rates of extinction, distribution, and protection, Science, 344, 1246752, 10.1126/science.1246752 Hopkins, 1935, Attachment of larvae of the Olympia oyster, Ostrea lurida, to plane surfaces, Ecology, 16, 82, 10.2307/1932859 Frobius, 2017, Rotiferan Hox genes give new insights into the evolution of metazoan bodyplans, Nat Commun, 8, 9, 10.1038/s41467-017-00020-w Shiga, 2002, Evolving role of Antennapedia protein in arthropod limb patterning, Development, 129, 3555, 10.1242/dev.129.15.3555 Khadjeh, 2012, Divergent role of the Hox gene Antennapedia in spiders is responsible for the convergent evolution of abdominal limb repression, Proc Natl Acad Sci U S A, 109, 4921, 10.1073/pnas.1116421109 Kimoto, 2014, Hox transcription factor Antp regulates sericin-1 gene expression in the terminal differentiated silk gland of Bombyx mori, Dev Biol, 386, 64, 10.1016/j.ydbio.2013.12.002 Metzler, 2016, Composition and structure of oyster adhesive reveals heterogeneous materials properties in a biological composite, Adv Funct Mater, 26, 6814, 10.1002/adfm.201602348 Guerette, 2013, Accelerating the design of biomimetic materials by integrating RNA-seq with proteomics and materials science, Nat Biotechnol, 31, 908, 10.1038/nbt.2671 Ji, 2006, SK Ca2+-activated K+ channel ligands alter the firing pattern of dopamine-containing neurons in vivo, Neuroscience, 140, 623, 10.1016/j.neuroscience.2006.02.020 Hennebert, 2015, Experimental strategies for the identification and characterization of adhesive proteins in animals: a review, Interface Focus, 5, 20140064, 10.1098/rsfs.2014.0064 Li, 2007, Epidermal secretions of terrestrial flatworms and slugs: Lehmannia valentiana mucus contains matrilin-like proteins, Comp Biochem Physiol B Biochem Mol Biol, 148, 231, 10.1016/j.cbpb.2007.06.001 Hennebert, 2014, Sea star tenacity mediated by a protein that fragments, then aggregates, Proc Natl Acad Sci U S A, 111, 6317, 10.1073/pnas.1400089111 Lee, 2011, Mussel-inspired adhesives and coatings, Annu Rev Mater Res, 41, 99, 10.1146/annurev-matsci-062910-100429 Rucker, 1998, Copper, lysyl oxidase, and extracellular matrix protein cross-linking, Am J Clin Nutr, 67, 996S, 10.1093/ajcn/67.5.996S Walker, 1971, A study of the cement apparatus of the cypris larva of the barnacle Balanus balanoides, Mar Biol, 9, 205, 10.1007/BF00351380 Smith, 2013, Multiple Metal-based Cross-Links: Protein Oxidation And Metal Coordination In a Biological Glue, 3 Coon, 1990, Competence and delay of metamorphosis in the Pacific oyster Crassostrea gigas, Mar Biol, 106, 379, 10.1007/BF01344316 Bonar, 1990, Control of oyster settlement and metamorphosis by endogenous and exogenous chemical cues, B Mar Sci, 46, 484 Wang, 2015, Voltage-gated potassium ion channel may play a major role in the settlement of Pacific oyster (Crassostrea gigas) larvae, Aquaculture, 442, 48, 10.1016/j.aquaculture.2015.02.033 Foulon, 2019, In silico analysis of Pacific oyster (Crassostrea gigas) transcriptome over developmental stages reveals candidate genes for larval settlement, Int J Mol Sci, 20, 197, 10.3390/ijms20010197 Zhang, 2017, Crystal structures of a ZIP zinc transporter reveal a binuclear metal center in the transport pathway, Sci Adv, 3, 10.1126/sciadv.1700344 Du, 2011, Biosorption of divalent Pb, Cd and Zn on aragonite and calcite mollusk shells, Environ Pollut, 159, 1763, 10.1016/j.envpol.2011.04.017 Bond, 1995, The astacin family of metalloendopeptidases, Protein Sci, 4, 1247, 10.1002/pro.5560040701 Sadeghi, 2000, Symmetry and limb dominance in able-bodied gait: a review, Gait Posture, 12, 34, 10.1016/S0966-6362(00)00070-9 Weiss, 2006, The distribution of chitin in larval shells of the bivalve mollusk Mytilus galloprovincialis, J Struct Biol, 153, 264, 10.1016/j.jsb.2005.11.006 Marin, 2008, Molluscan shell proteins: primary structure, origin, and evolution, Curr Top Dev Biol, 80, 209, 10.1016/S0070-2153(07)80006-8 Splitt, 1996, Defects in the determination of left-right asymmetry, J Med Genet, 33, 498, 10.1136/jmg.33.6.498 Savazzi, 1982, Adaptational strategies of bivalves living as infaunal secondary soft bottom dwellers, Neues Jahrb Geol P-A, 164, 229, 10.1127/njgpa/164/1982/229 Wilbur, 1983, Shell Formation, 235 Yoshioka, 1998, Pitx2, a bicoid-type homeobox gene, is involved in a lefty-signaling pathway in determination of left-right asymmetry, Cell, 94, 299, 10.1016/S0092-8674(00)81473-7 Grande, 2009, Nodal signalling is involved in left-right asymmetry in snails, Nature, 457, 1007, 10.1038/nature07603 Smith, 2010, Rfx6 directs islet formation and insulin production in mice and humans, Nature, 463, 775, 10.1038/nature08748 Hamano, 2005, cDNA structure of an insulin-related peptide in the Pacific oyster and seasonal changes in the gene expression, J Endocrinol, 187, 55, 10.1677/joe.1.06284 Nagai, 2007, Tyrosinase localization in mollusc shells, Comp Biochem Physiol B Biochem Mol Biol, 146, 207, 10.1016/j.cbpb.2006.10.105 Gnerre, 2011, High-quality draft assemblies of mammalian genomes from massively parallel sequence data, Proc Natl Acad Sci U S A, 108, 1513, 10.1073/pnas.1017351108 Boetzer, 2011, Scaffolding pre-assembled contigs using SSPACE, Bioinformatics, 27, 578, 10.1093/bioinformatics/btq683 Luo, 2015, Erratum: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler, Gigascience, 4, 30, 10.1186/s13742-015-0069-2 Koren, 2017, Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation, Genome Res, 27, 722, 10.1101/gr.215087.116 Salmela, 2014, LoRDEC: accurate and efficient long read error correction, Bioinformatics, 30, 3506, 10.1093/bioinformatics/btu538 Parra, 2007, CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes, Bioinformatics, 23, 1061, 10.1093/bioinformatics/btm071 Simao, 2015, BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs, Bioinformatics, 31, 3210, 10.1093/bioinformatics/btv351 Lieberman-Aiden, 2009, Comprehensive mapping of long-range interactions reveals folding principles of the human genome, Science, 326, 289, 10.1126/science.1181369 Burton, 2013, Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions, Nat Biotechnol, 31, 1119, 10.1038/nbt.2727 Li, 2018, Construction of a high-density genetic map and fine QTL mapping for growth and nutritional traits of Crassostrea gigas, BMC Genomics, 19, 626, 10.1186/s12864-018-4996-z Wicker, 2007, A unified classification system for eukaryotic transposable elements, Nat Rev Genet, 8, 973, 10.1038/nrg2165 Bao, 2015, Repbase Update, a database of repetitive elements in eukaryotic genomes, Mob DNA, 6, 11, 10.1186/s13100-015-0041-9 Chen N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinformatics 2009;Chapter 4:Unit 4.10. Burge, 1997, Prediction of complete gene structures in human genomic DNA, J Mol Biol, 268, 78, 10.1006/jmbi.1997.0951 Stanke, 2003, Gene prediction with a hidden Markov model and a new intron submodel, Bioinformatics, 19, ii215, 10.1093/bioinformatics/btg1080 Majoros, 2004, TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders, Bioinformatics, 20, 2878, 10.1093/bioinformatics/bth315 Blanco E, Parra G, Guigo R. Using geneid to identify genes. Curr Protoc Bioinformatics 2007;Chapter 4:Unit 4.3. Korf, 2004, Gene finding in novel genomes, BMC Bioinformatics, 5, 59, 10.1186/1471-2105-5-59 Keilwagen, 2016, Using intron position conservation for homology-based gene prediction, Nucleic Acids Res, 44, 10.1093/nar/gkw092 Haas, 2008, Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments, Genome Biol, 9, R7, 10.1186/gb-2008-9-1-r7 Conesa, 2005, Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research, Bioinformatics, 21, 3674, 10.1093/bioinformatics/bti610 Nam, 2017, Genome sequence of pacific abalone (Haliotis discus hannai): the first draft genome in family Haliotidae, Gigascience, 6, 1, 10.1093/gigascience/gix014 Li, 2003, OrthoMCL: identification of ortholog groups for eukaryotic genomes, Genome Res, 13, 2178, 10.1101/gr.1224503 Edgar, 2004, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, 32, 1792, 10.1093/nar/gkh340 Stamatakis, 2014, RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, 30, 1312, 10.1093/bioinformatics/btu033 Yang, 2007, PAML 4: phylogenetic analysis by maximum likelihood, Mol Biol Evol, 24, 1586, 10.1093/molbev/msm088 De Bie, 2006, CAFE: a computational tool for the study of gene family evolution, Bioinformatics, 22, 1269, 10.1093/bioinformatics/btl097 Albertin, 2015, The octopus genome and the evolution of cephalopod neural and morphological novelties, Nature, 524, 220, 10.1038/nature14668 Keilwagen, 2019, GeMoMa: homology-based gene prediction utilizing intron position conservation and RNA-seq data, Methods Mol Biol, 1962, 161, 10.1007/978-1-4939-9173-0_9 Trapnell, 2009, TopHat: discovering splice junctions with RNA-Seq, Bioinformatics, 25, 1105, 10.1093/bioinformatics/btp120 Trapnell, 2012, Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Nat Protoc, 7, 562, 10.1038/nprot.2012.016 Langfelder, 2008, WGCNA: an R package for weighted correlation network analysis, BMC Bioinformatics, 9, 559, 10.1186/1471-2105-9-559 Coon, 1986, Chemical production of cultchless oyster spat using epinephrine and norepinephrine, Aquaculture, 58, 255, 10.1016/0044-8486(86)90090-6 Chen, 2021, The Genome Sequence Archive Family: toward explosive data growth and diverse data types, Genomics Proteomics Bioinformatics, 19, 578, 10.1016/j.gpb.2021.08.001 Chen, 2021, Genome Warehouse: a public repository housing genome-scale data, Genomics Proteomics Bioinformatics, 19, 584, 10.1016/j.gpb.2021.04.001