Nascent transcription reveals regulatory changes in extremophile fishes inhabiting hydrogen sulfide-rich environments

Regulating transcription allows organisms to respond to their environment, both within a single generation (plasticity) and across generations (adaptation). We examined transcriptional differences in gill tissues of fishes in the Poecilia mexicana species complex (family Poeciliidae), which have colonized toxic springs rich in hydrogen sulfide (H2S) in southern Mexico. There are gene expression differences between sulfidic and non-sulfidic populations, yet regulatory mechanisms mediating this gene expression variation remain poorly studied. We combined capped-small RNA sequencing (csRNA-seq), which captures actively transcribed (i.e., nascent) transcripts, and traditional messenger RNA sequencing (mRNA-seq) to examine how variation in transcription, enhancer activity, and associated transcription factor binding sites may facilitate adaptation to extreme environments. csRNA-seq revealed thousands of differentially initiated transcripts between sulfidic and non-sulfidic populations, many ..., Sample collection
Adult female fish were collected via seine net from sulfidic and non-sulfidic sites in the Pichucalco, Puyacatengo, and Tacotalpa drainages of the Río Grijalva basin in southern Mexico (N = 5–6 per site; electronic supplementary material, table S1) as part of a previous study by Kelley et al. (Kelley et al., 2016). In the Pichucalco drainage, sulfidic springs are inhabited by the highly endemic extremophile Poecilia sulphuraria (sulphur molly; figure 1b, top) (Alvarez del Villar, 1948), but non-sulfidic springs are populated by P. mexicana (figure 1b, bottom). In the Puyacatengo and Tacotalpa drainages, P. mexicana inhabits both the sulfidic and non-sulfidic sites (figure 1c–d). Fish were sacrificed, and their gill arches were extracted, preserved in RNAlater (Invitrogen, Inc), and stored at -80 ºC. Gill tissues were selected because they are directly exposed to H2S in the water and were previously shown to have significant gene expression differences between the sulfi..., , # Data from: Nascent transcription reveals regulatory changes in extremophile fishes inhabiting hydrogen sulfide-rich environments

This repo contains code for all data processing and analysis used in our study of transcription and gene expression in H2S-adapted populations of *P. mexicana*.

## Description of Data and File Structure

### Table\_S5\_01.30.24.xlsx

* **csRNA Peak ID:** The identifier assigned to the csRNA-seq peak.
* **Chromosome:** The chromosomal scaffold in the *P. mexicana* reference genome the peak mapped to.
* **Start:** The start coordinate of the peak.
* **End:** The end coordinate of the peak.
* **Strand:** Strand (+/-) the read mapped to.
* **Annotation:** The type of genomic element the read mapped to [e.g., intergenic, intron, exon, promoter-transcription start site (TSS), transcription termination site (TTS)].
* **Nearest Gene:** The name of the closest annotated gene to the peak.
* **Distance to TSS (bp):** The distance in base pairs (bp) to...