Temperature-dependent gene regulatory divergence underlies local adaptation with gene flow in the Atlantic silverside

Gene regulatory divergence is thought to play an important role in adaptation, yet its extent and underlying mechanisms remain largely elusive for local adaptation with gene flow. Local adaptation is widespread in marine species despite generally high connectivity and is often associated with tightly linked genomic architectures, such as chromosomal inversions. To investigate gene regulatory evolution under gene flow and the role of inversions associated with local adaptation to a steep thermal gradient, we generated RNA-seq data from Atlantic silversides (Menidia menidia) from two locally adapted populations and their F1 hybrids, reared under two temperatures. We found substantial divergence in gene expression and thermal plasticity between populations, with up to 31% of genes being differentially expressed. Reduced thermal plasticity, temperature-dependent gene misexpression and the disruption of co-expression networks in hybrids point towards a role of regulatory incompatibilities in..., To improve the contiguity of the Atlantic silverside reference genome (Tigano et al. 2021), we anchored the genome assembly to a RAD-seq based female Georgia linkage map (Akopyan et al. 2022). However, the linkage map used for this assembly differs marginally from the one in Akopyan et al. (2022), as it was constructed from genome-aligned RAD-seq data rather than de novo assembled loci. Overall, both linkage maps are highly comparable. The linkage map was constructed as described in Akopyan et al. (2022) with slight modifications outlined here:
            In brief, we used ddRAD sequencing (Peterson et al. 2012) to identify and genotype single nucleotide polymorphisms (SNPs) for linkage map construction from ​​568 individuals across five families, including the two founders, 138 F1 offspring, six additional F1 siblings and their 282 F2 offspring. Reads were processed in Stacks v1.48 (Catchen et al. 2013) with the module process_radtags to discard low-quality reads and reads with ambigu..., , # Temperature-dependent gene regulatory divergence underlies local adaptation with gene flow in the Atlantic silverside

[https://doi.org/10.5061/dryad.76hdr7t3s](https://doi.org/10.5061/dryad.76hdr7t3s)

## Description of the data and file structure

1. Mmenidia_refgenome_anchored.all_renamed_v2.fasta: Reference genome scaffolds for Menidia menidia anchored to a consensus linkage map. See Methods section and Supplementary material for detailed methods.
2. mme_annotation_anchored_genome_final_clean.noseq.gff: Gene annotation for the anchored reference genome. Output from Maker.
3. mme_protein_blast2go_annot_topGO.annot: Gene ontology annotation (from Blast2GO) used for GO overrepresentation analysis using topGO
4. mme_blast2go_annotation_descriptions.txt: Functional annotation (from Blast2GO) of genes annotated in Menidia menidia genome.

基因调控分化被认为在适应性演化中扮演重要角色，但针对存在基因流的局部适应性而言，其具体程度与潜在机制仍基本未被阐明。局部适应性在海洋物种中广泛存在，尽管这类物种通常具有较高的连通性，且其局部适应性常与染色体倒位等紧密连锁的基因组结构相关。为探究存在基因流时的基因调控演化，以及与适应陡峭温度梯度的局部适应性相关的倒位所发挥的作用，我们针对两个本地适应种群及其F1杂交个体开展了实验，在两种温度条件下饲养后获取了RNA-seq（RNA测序）数据。结果显示，种群间在基因表达与热可塑性上存在显著分化，多达31%的基因呈现差异表达。杂交个体中出现的热可塑性降低、温度依赖的基因表达异常，以及共表达网络的破坏，均提示调控不相容性在……。为提升大西洋银汉鱼（Menidia menidia）参考基因组（Tigano et al. 2021）的连续性，我们将该基因组组装锚定至基于RAD-seq（限制性位点关联DNA测序）构建的雌性佐治亚州连锁图谱（Akopyan et al. 2022）。不过本次组装所用的连锁图谱与Akopyan等（2022）的图谱存在细微差异：本次图谱是基于基因组比对的RAD-seq数据构建，而非从头组装的位点。总体而言，两种连锁图谱具有高度可比性。连锁图谱的构建参照Akopyan等（2022）的方法，并在此进行了小幅修改：简言之，我们采用ddRAD测序（Peterson et al. 2012）来鉴定与分型单核苷酸多态性（Single Nucleotide Polymorphism, SNP），以用于连锁图谱构建，样本来自5个家系的568个个体，包括两个亲本、138个F1后代、6个额外的F1同胞个体以及282个F2后代。测序reads通过Stacks v1.48（Catchen et al. 2013）的process_radtags模块进行处理，以丢弃低质量reads与带有歧义序列的reads……

# 温度依赖的基因调控分化是大西洋银汉鱼存在基因流时局部适应性的基础

https://doi.org/10.5061/dryad.76hdr7t3s

## 数据与文件结构说明
1. Mmenidia_refgenome_anchored.all_renamed_v2.fasta：锚定至共识连锁图谱的大西洋银汉鱼参考基因组支架序列，详细方法参见方法部分与补充材料。
2. mme_annotation_anchored_genome_final_clean.noseq.gff：锚定参考基因组的基因注释文件，为Maker软件的输出结果。
3. mme_protein_blast2go_annot_topGO.annot：用于通过topGO开展基因本体（GO）富集分析的基因本体注释文件（源自Blast2GO）。
4. mme_blast2go_annotation_descriptions.txt：大西洋银汉鱼基因组注释基因的功能注释文件（源自Blast2GO）。