DOI: 10.5061/dryad.zpc866tf1
title: Spatial-temporal expression analysis of lineage-restricted shell matrix proteins in the slipper snail Crepidula atrasolea reveals shell field regionalization and distinct cell populations

description: Mollusca is a morphologically diverse metazoan phylum, exhibiting an
 immense variety of calcium carbonate shells. Biomineralization of the
 shell involves shell matrix proteins (SMPs). While SMP diversity is
 hypothesized to drive molluscan shell diversity, we are just starting to
 unravel SMP evolutionary history and biology. Here we leveraged two
 complementary molluscan model systems, the marine slipper snails Crepidula
 fornicata and Crepidula atrasolea, to determine the evolutionary lineage
 of 185 Crepidula SMPs. We found that 95% of the adult C. fornicata shell
 proteome belongs to conserved metazoan and molluscan orthogroups, with
 molluscan-restricted orthogroups containing half of all SMPs in the shell
 proteome. The low number of C. fornicata-restricted SMPs contradicts the
 generally-held notion that an animal’s biomineralization toolkit is
 dominated by mostly novel genes. Next, we selected a subset of SMPs across
 evolutionary lineages for spatial-temporal analysis using in situ
 hybridization chain reaction (HCR) during shell development in C.
 atrasolea. We found that 12 out of the 18 SMPs we analyzed are expressed
 in the shell tissue. These transcripts are present in 5 expression
 patterns, which define at least three distinct cell populations within the
 shell field. These results represent the most comprehensive analysis of
 gastropod SMP evolutionary age and shell field expression patterns to
 date. Collectively, these data lay the foundation for future work to
 interrogate the molecular mechanisms and cell fate decisions underlying
 molluscan mantle specification and diversification. 
description: # Spatial-temporal expression analysis of lineage-restricted shell matrix
 proteins in the slipper snail Crepidula atrasolea reveals shell field
 regionalization and distinct cell populations
 [https://doi.org/10.5061/dryad.zpc866tf1](https://doi.org/10.5061/dryad.zpc866tf1) Orthofinder2 and Kinfin results run on April 2024. ## 1. Orthofinder Dataset * `Results_Apr17.tar.gz`: Part 1 Orthofinder results (submit with -og: Stop after inferring orthogroups). Script `2_ortho_infer_orthogroups.sh` was used to run this step. * Comparative_Genomics_Statistics * Orthogroups * Orthogroup_Sequences * Single_Copy_Orthologue_Sequences * `Results_Apr27.tar.gz`: Part 2 Orthofinder results (submit with -fg: Start analysis from orthogroups OrthoFinder directory) and -ot ( Stop after inferring gene trees for orthogroups). Script `3_ortho_infer_gene_trees.sh` * Gene_Trees * MultipleSequenceAlignments * Orthogroup_Sequences * Orthologues * `Results_Apr29_1.tar.gz`: Part 3 Orthofinder results (submit with -ft: Start analysis from gene trees in OrthoFinder directory). Script `4_rooted_gene_trees.sh` * Gene_Duplication_Events * Orthologues * Phylogenetic_Hierarchial_Orthogroups * Resolve_Gene_Trees * Comparative_Genomics_Statistics * Phylogenetically_Misplaced_Genes * Putative_Xenologs * Species_Tree * `Proteomes-Apr2024.tar.gz`: Fasta files for 95 species proteomes used to run the orthofinder analysis.  * `SMP_trees.tar.gz`: SMP gene trees for 185 SMPs from Crepidula fornicata and their multiple sequence alignment (MSA) files. * smp-tree: Directory containing SMP orthogroup gene trees * smp-msa: Directory containing SMP orthogroup multiple sequence alignments * `Ortho_scripts.tar.gz`: Commands used to run orthofinder analysis * 1_copy_proteomes_april2024.sh * 2_ortho_infer_orthogroups.sh * 3_ortho_infer_gene_trees.sh * 4_rooted_gene_trees.sh ## 2. Kinfin Dataset * `kinfin.tar.gz`: Kinfin results and evolutionary analysis of SMP lineage-restricted genes * kinfin_results * Analysis * class * family * genus * order * phylum * superfamily * TAXON * tree * 185-SMPs * class-kinfin-output * genus-kinfin-output * TAXON-kinfin-output * family-kinfin-output * order-kinfin-output * phylum-kinfin-output * superfamily-kinfin-output * `kinfin_scripts.tar.gz`: Commands used to run kinfin analysis * 1_submit_kinfin.sh * 2_post.kinfin.sh ## 3. Hybrid Transcriptome * `10_original_Catra_transcripts_stranded_cdhit95_stranded_noAlien.fasta`: Nucleotide transcriptome for C. atrasolea. Uploaded and accepted to NCBI/TSA (GKTO01000000) * `10_original_Catra_transcripts_stranded_cdhit95_stranded_noAlien.pep`: Translated proteome of hybrid transcriptome for C. atrasolea. Used in orthofinder analysis