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| Status |
Public on Jul 02, 2025 |
| Title |
The genomic origin of the unique chaetognath body plan |
| Organism |
Paraspadella gotoi |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
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| Summary |
The emergence of animal phyla, each with their unique body plan, was a rapid event in the history of animal life, yet its genomic underpinnings are still poorly understood. Here, we investigate at the genomic, regulatory, and cellular levels the origin of one of the most enigmatic animal phyla, the chaetognaths, whose distinctive organismal characteristics have historically complicated its phylogenetic placement. We show that some of these characteristics are reflected at the cell-type level by the expression of genes originating in the chaetognath lineage, contributing to adaptation to planktonic life at the sensory and structural levels. Chaetognaths belong to the gnathiferan lineage (also including rotifers and several other microscopic phyla), which is marked by accelerated genomic evolution with gene loss and chromosomal rearrangements. Chaetognaths further secondarily acquired thousands of newly duplicated genes, without evidence for a whole genome duplication, yielding, for instance, tandemly expanded Hox genes, as well as many phylum-specific genes. We also detected repeat-rich highly-methylated neocentromeres and a simplified DNA methylation toolkit, which is involved in mobile element repression rather than transcriptional control, a role inherited by trans-splicing. Consistent with fossil evidence, our observations suggest that chaetognaths emerged after a phase of morphological simplification through a reinvention of organ systems paralleled by massive genomic reorganisation, explaining the uniqueness of the chaetognath body plan.
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| Overall design |
scRNA-seq, ATAC-seq, RNA-seq and EM-seq to characterise gene regulation
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| Contributor(s) |
Piovani L, Gavriouchkina D, Goto T, Marlétaz F, Sarre L, Mendoza A |
| Citation(s) |
40804517 |
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| Submission date |
Oct 15, 2024 |
| Last update date |
Oct 01, 2025 |
| Contact name |
Ferdinand Marlétaz |
| E-mail(s) |
ferdinand.marletaz@gmail.com
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| Organization name |
University College London
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| Department |
Genetics, Evolution & Environment
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| Street address |
Gower Street
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| City |
London |
| ZIP/Postal code |
WC1E 6BT |
| Country |
United Kingdom |
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| Platforms (2) |
| GPL34994 |
Illumina NovaSeq X (Paraspadella gotoi) |
| GPL34995 |
Illumina NovaSeq 6000 (Paraspadella gotoi) |
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| Samples (13)
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| GSM8573296 |
10x 3' mRNA single-cell, Adult, sample22, whole animal |
| GSM8573297 |
10x 3' mRNA single-cell, Adult, sample1, whole animal |
| GSM8573298 |
10x 3' mRNA single-cell, Hatchling, sample, whole animal |
| GSM8573299 |
ATAC-seq, adult, whole animal, sample 1 |
| GSM8573300 |
ATAC-seq, adult, whole animal, sample 2 |
| GSM8573301 |
ATAC-seq, adult, whole animal, sample 3 |
| GSM8573302 |
ATAC-seq, hatchling, whole animal, sample 1 |
| GSM8573303 |
ATAC-seq, hatchling, whole animal, sample 2 |
| GSM8573304 |
EM-seq, whole adult |
| GSM8573305 |
RNA-seq, whole adult |
| GSM8573306 |
RNA-seq, low input, 3 days hatchling, whole |
| GSM8573307 |
RNA-seq, low input, gastrula, whole |
| GSM8573308 |
RNA-seq, low input, 1day hatchling, whole |
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| Relations |
| BioProject |
PRJNA1173127 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE279488_Pgot_lowinput_SLs_counts_eq.tsv.gz |
1.6 Mb |
(ftp)(http) |
TSV |
| GSE279488_RAW.tar |
978.9 Mb |
(http)(custom) |
TAR (of BW, CGMAP, MTX, TSV, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
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