Comparative analysis of the morphology, karyotypes and biochemical composition of muscle in Siniperca chuatsi, Siniperca scherzeri and the F1 hybrid (S. chuatsi ♀ × S. scherzeri ♂)

Guan, Wenzhi; Qiu, Gao‐Feng; Liu, Feng

doi:10.1016/j.aaf.2020.07.020

Cited by 2 publications

(2 citation statements)

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“…Siniperca chuatsi and S. scherzeri differ in several phenotypic traits. First, the two species are divergent in body length, body width, and skin pigmentation ( Figure 1A , B) ( Guan et al, 2022 ). Second, S. chuatsi exhibits a substantially higher growth rate than S. scherzeri but is also more susceptible to disease ( Ding et al, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Long-read genome assemblies reveal a cis-regulatory landscape associated with phenotypic divergence in two sister Siniperca fish species

Tu¹,

Zhang²,

Jiang³

et al. 2023

Zoological Research

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Due to the difficulty in accurately identifying structural variants (SVs) across genomes, their impact on cis -regulatory divergence of closely related species, especially fish, remains to be explored. Recently identified broad H3K4me3 domains are essential for the regulation of genes involved in several biological processes. However, the role of broad H3K4me3 domains in phenotypic divergence remains poorly understood. Siniperca chuatsi and S. scherzeri are closely related but divergent in several phenotypic traits, making them an ideal model to study cis -regulatory evolution in sister species. Here, we generated chromosome-level genomes of S. chuatsi and S. scherzeri , with assembled genome sizes of 716.35 and 740.54 Mb, respectively. The evolutionary histories of S. chuatsi and S. scherzeri were studied by inferring dynamic changes in ancestral population sizes. To explore the genetic basis of adaptation in S. chuatsi and S. scherzeri , we performed gene family expansion and contraction analysis and identified positively selected genes (PSGs). To investigate the role of SVs in cis -regulatory divergence of closely related fish species, we identified high-quality SVs as well as divergent H3K27ac and H3K4me3 domains in the genomes of S. chuatsi and S. scherzeri . Integrated analysis revealed that cis -regulatory divergence caused by SVs played an essential role in phenotypic divergence between S. chuatsi and S. scherzeri . Additionally, divergent broad H3K4me3 domains were mostly associated with cancer-related genes in S. chuatsi and S. scherzeri and contributed to their phenotypic divergence.

show abstract

Section: Introductionmentioning

confidence: 99%

Long-read genome assemblies reveal a cis-regulatory landscape associated with phenotypic divergence in two sister Siniperca fish species

Tu¹,

Zhang²,

Jiang³

et al. 2023

Zoological Research

View full text Add to dashboard Cite

show abstract

“…Siniperca chuatsi and S. scherzeri diverged in several phenotypic traits. First, the two species are divergent in body length, body width, and skin pigmentation ( Figure 1A and B ) [24]. Second, the growth rate of S. chuatsi is substantially higher than that of S. scherzeri , while S. chuatsi is more susceptible to disease than S. scherzeri [25].…”

Section: Introductionmentioning

confidence: 99%

Long-read genome assemblies reveals acis-regulatory landscape associated with phenotypic divergence in two sisterSinipercafishes

Chen

Zhang

et al. 2022

Preprint

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Background: Dissecting the genetic basis of variation in the regulation of gene expression is essential for understanding phenotypic evolution. Structural variants intersecting the cis-regulatory elements are found to cause gene expression variation in several developmental genes, resulting in morphological divergence between species. Due to the difficulty of identifying structural variants accurately across the genome, a comprehensive study of impacts of structural variants in cis-regulatory divergence of closely related species, especially fish species, is still scarce. Recently identified broad H3K4me3 domains are essential for the regulation of genes involved in several biological processes. However, the role of broad H3K4me3 domains in phenotypic divergence remain poorly understood. Siniperca chuatsi and S. scherzeri are two closely related fish species diverge in several phenotypic traits, making them an ideal model to study cis-regulatory evolution in closely related species. Results: We generated chromosome-level genomes of S. chuatsi and S. scherzeri. The evolutionary histories of S. chuatsi and S. scherzeri were studied by inferring the dynamic changes in the ancestral population sizes. The genetic basis of adaptation in S. chuatsi and S. scherzeri was dissected by performing gene family expansion and contraction analysis and identifying positively selected genes (PSGs). To investigate the role of SVs in cis-regulatory divergence of closely related fish species, we identified high-quality SVs between S. chuatsi and S. scherzeri, as well as H3K27ac and H3K4me3 domains. Integrated analysis revealed that cis-regulatory divergence caused by SVs played an essential role in the differentiation of metabolism, skin pigmentation, and immunity between S. chuatsi and S. scherzeri. Additionally, divergent broad H3K4me3 domains were found to mostly associate with cancer-related genes in S. chuatsi and S. scherzeri and contribute to their phenotypic divergence. Conclusions: Our analysis reveals SVs play an essential role in cis-regulatory variation between the two sister fish species, which in turn contributes to their phenotypic divergence. The divergence of broad H3K4me3 domains contributes to phenotypic divergence between closely related species. Additionally, the association of broad H3K4me3 domains and cancer-related genes has an ancient origin.

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Comparative analysis of the morphology, karyotypes and biochemical composition of muscle in Siniperca chuatsi, Siniperca scherzeri and the F1 hybrid (S. chuatsi ♀ × S. scherzeri ♂)

Cited by 2 publications

References 26 publications

Long-read genome assemblies reveal a <i>cis</i>-regulatory landscape associated with phenotypic divergence in two sister <i>Siniperca</i> fish species

Long-read genome assemblies reveal a <i>cis</i>-regulatory landscape associated with phenotypic divergence in two sister <i>Siniperca</i> fish species

Long-read genome assemblies reveals acis-regulatory landscape associated with phenotypic divergence in two sisterSinipercafishes

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