Single cell RNA sequencing provides clues for the developmental genetic basis of Syngnathidae’s evolutionary adaptations
Data files
Oct 18, 2024 version files 698.93 MB
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GCF_024217435.1_RoL_Ssco_1.1_genomic.MT-Lin.fna
433.87 MB
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genemodels_sscncbi_emb_pouch_LINMT.gtf
265.06 MB
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README.md
1.79 KB
Abstract
Seahorses, pipefishes, and seadragons are fishes from the family Syngnathidae that have evolved extraordinary traits including male pregnancy, elongated snouts, loss of teeth, and dermal bony armor. The developmental genetic and cellular changes that led to the evolution of these traits are largely unknown. Recent syngnathid genomes revealed suggestive gene content differences and provide the opportunity for detailed genetic analyses. We created a single cell RNA sequencing atlas of Gulf pipefish embryos to understand the developmental basis of four traits: derived head shape, toothlessness, dermal armor, and male pregnancy. We completed marker gene analyses, built genetic networks, and examined spatial expression of select genes. We identified osteochondrogenic mesenchymal cells in the elongating face that express regulatory genes bmp4, sfrp1a, and prdm16. We found no evidence for tooth primordia cells, and we observed re-deployment of osteoblast genetic networks in developing dermal armor. Finally, we found that epidermal cells expressed nutrient processing and environmental sensing genes, potentially relevant for the brooding environment. The examined pipefish evolutionary innovations are composed of recognizable cell types, suggesting derived features originate from changes within existing gene networks. Future work addressing syngnathid gene networks across multiple stages and species is essential for understanding how their novelties evolved.
https://doi.org/10.5061/dryad.f7m0cfz60
Description of the data and file structure
These files were modified in order to analyze single cell RNA sequencing libraries produced from Syngnathus scovelli embryos
Files and variables
File: GCF_024217435.1_RoL_Ssco_1.1_genomic.MT-Lin.fna
Description: This fasta file contains two fasta files appended together: GCF024217435.1 (Syngnathus scovelli nuclear genome) and NC065499.1 (Syngnathus scovelli mitochondria genome).
File: genemodels_sscncbi_emb_pouch_LINMT.gtf
Description: The gene models from this file consists of annotations from GCF024217435.1 (Syngnathus scovelli nuclear genome annotation), NC065499.1 (Syngnathus scovelli mitochondria genome annotation), and annotations derived from scISOrSeq data. These annotations were merged together using TAMA merge.
Code/software
The fasta files were appended together using cat. The merged annotation file was produced following the pipeline from Healey et al. 2022. To analyze the scISOrSeq reads, sequences were processed using scripts from Healey et al. 2022, aligned with minimap v2.9, and gene models were derived with SQANTI3. The annotation files were merged with TAMA merge.
Access information
Other publicly accessible locations of the data:
- scRNAseq reads and the processed dataset is available on GSE278814
Data was derived from the following sources:
- GCA_024217435.2 (Synganthus scovelli nuclear genome)
- NC_065499.1 (Syngnathus scovelli mitochondrial genome)
The fasta file and annotation file shared here were used in the single cell RNA sequencing analysis described in the publication. The fasta nuclear genome file was downloaded from NCBI (GCF_024217435.2). The mitochondrial genome fasta file was downloaded from NCBI (NC_065499.1). The two fasta files were appended together to create the fasta file used in the analysis. To lengthen the 3' UTRs of the genome annotations, we produced two scISOrSeq libraries (one from a late embryonic stage and one from pregnant and non-pregnant brood pouch tissues) that were sequenced on seperate lanes on PacBio Sequel II - SMRT cells 8M. Reads were processed according to Healey et al. 2022 and aligned with the Gulf pipefish genome (GCF_024217435.2). Gene models from the scISOrSeq datasets were merged with the Gulf pipefish NCBI models (GCF_024217435.2) using TAMA merge.