Spatial-temporal expression analysis of lineage-restricted shell matrix proteins in the slipper snail Crepidula atrasolea reveals shell field regionalization and distinct cell populations

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 hybri..., , , # 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_Apr...