Alternatively spliced variants in Atlantic cod (Gadus morhua) support response to variable salinity environment

Kijewska, Agnieszka; Malachowicz, Magdalena; Wenne, Roman

doi:10.1038/s41598-018-29723-w

Cited by 12 publications

(13 citation statements)

References 59 publications

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“…In muscle, brain, and gut, we also found several ASGs whose function may be involved in the cellular response to stresses (e.g., oxidative stress and DNA damage). Thus, our study supports that AS can act as an efficient mechanism in responding to environmental or cellular stresses, which has been extensively implicated in both animals and plants (Grantham & Brisson, 2018 ; Ibrahim et al., 2021 ; Kijewska et al., 2018 ). More importantly, our current study further indicates that AS may play a more important role than gene expression regulation in coping with the severe cellular stress in nature (see also Singh et al., 2017 ; Jacobs & Elmer, 2021 ; Martín et al., 2021 ).…”

Section: Discussionsupporting

confidence: 84%

“…Changes in gene expression have been widely implicated in the rapid adaptation to variable environmental stresses (Fraser, 2013 ; Hodgins‐Davis & Townsend, 2009 ; Kenkel & Matz, 2016 ; Lasky et al., 2014 ; López‐Maury et al., 2008 ; Rivera et al., 2021 ), phenotypic variations (Hodgins‐Davis & Townsend, 2009 ; Kaern et al., 2005 ; Mank, 2017 ), and adaptive radiations (Barrier et al., 2001 ; El Taher et al., 2021 ; Whittall et al., 2006 ). Alternative splicing (AS), a mechanism of creating multiple isoforms from a single gene, offers another route for organisms to respond to environmental stresses rapidly and efficiently (Kijewska et al., 2018 ; Smith et al., 2018 ) and has also been associated with phenotypic variations in eukaryotes (Bush et al., 2017 ; Grantham & Brisson, 2018 ). Compared with gene expression regulation, AS has been proposed to play a more important role in facilitating rapid adaptive divergence within short timescales (Jacobs & Elmer, 2021 ; Singh et al., 2017 ).…”

Section: Introductionmentioning

confidence: 99%

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Extensive alternative splicing triggered by mitonuclear mismatch in naturally introgressed Rhinolophus bats

Chen

Mao

2021

Ecology and Evolution

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Mitochondrial function needs strong interactions of mitochondrial and nuclear (mitonuclear) genomes, which can be disrupted by mitonuclear mismatch due to mitochondrial DNA (mtDNA) introgression between two formerly isolated populations or taxa. This mitonuclear disruption may cause severe cellular stress in mismatched individuals. Gene expression changes and alternative splicing (AS) are two important transcriptional regulations to respond to environmental or cellular stresses. We previously identified a naturally introgressed population in the intermediate horseshoe bat (Rhinolophus affinis). Individuals from this population belong to R. a. himalayanus and share almost identical nuclear genetic background; however, some of them had mtDNA from another subspecies (R. a. macrurus). With this unique natural system, we examined gene expression changes in six tissues between five mitonuclear mismatched and five matched individuals. A small number of differentially expressed genes (DEGs) were identified, and functional enrichment analysis revealed that most DEGs were related to immune response although some may be involved in response to oxidative stress. In contrast, we identified extensive AS events and alternatively spliced genes (ASGs) between mismatched and matched individuals. Functional enrichment analysis revealed that multiple ASGs were directly or indirectly associated with energy production in mitochondria which is vital for survival of organism. To our knowledge, this is the first study to examine the role of AS in responding to cellular stress caused by mitonuclear mismatch in natural populations. Our results suggest that AS may play a more important role than gene expression regulation in responding to severe environmental or cellular stresses.

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Section: Discussionsupporting

confidence: 84%

Section: Introductionmentioning

confidence: 99%

Extensive alternative splicing triggered by mitonuclear mismatch in naturally introgressed Rhinolophus bats

Chen

Mao

2021

Ecology and Evolution

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“…In addition, the degree of conservation of AS between O. brevibarba and Danio rerio was the highest. This result indicated that closer evolutionary relationships shared larger numbers of AS gene identities (Lu et al 2010; Kijewska et al 2018).…”

Section: Discussionmentioning

confidence: 97%

Analysis of Chromosomal Numbers, Mitochondrial Genome, and Full-Length Transcriptome of Onychostoma brevibarba

Fan

et al. 2019

Mar Biotechnol

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Onychostoma brevibarba is a new discovered species which is distributed in Xiang Jiang River of the middle Chang Jiang basin in Hunan Province, South China. In this study, the ploidy levels of O. brevibarba were confirmed by counting chromosomal numbers and analyzing karyotype. The complete mitochondrial genome of O. brevibarba was determined and analyzed. Besides, we firstly performed the full-length transcriptome of O. brevibarba derived from 5 different tissues using the PacBio SMRT sequencing. The result shows that O. brevibarba was a diploid with 48 chromosomes. The complete mitogenome of O. brevibarba was 16,602 bp in size and very similar (89.1–91.3%) to that of other Onychostoma species but was distinct from all congeners. The full-length transcriptome dataset of O. brevibarba comprised 120,239 unigenes. Among the unigenes, 91,542 were functionally annotated, whereas 26,794 were found to have two or more isoforms. This study could provide many new insights into cytology and molecular characteristics of O. brevibarba ; it laid the foundation for further exploration of the genomic signatures of species of Onychostoma . Electronic supplementary material The online version of this article (10.1007/s10126-019-09899-6) contains supplementary material, which is available to authorized users.

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“…A set of outlier SNPs was located close to or within the genes associated with osmoregulation, and genes related to hydration and the development of oocytes. The adaptation of an eastern Baltic population to the low salinity water has been confirmed experimentally [ 130 , 131 , 132 , 133 ].…”

Section: Genetic Structure Of Wild Populationsmentioning

confidence: 96%

Single Nucleotide Polymorphism Markers with Applications in Conservation and Exploitation of Aquatic Natural Populations

Wenne

2023

Animals

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An increasing number of aquatic species have been studied for genetic polymorphism, which extends the knowledge on their natural populations. One type of high-resolution molecular marker suitable for studying the genetic diversity of large numbers of individuals is single nucleotide polymorphism (SNP). This review is an attempt to show the range of applications of SNPs in studies of natural populations of aquatic animals. In recent years, SNPs have been used in the genetic analysis of wild and enhanced fish and invertebrate populations in natural habitats, exploited migratory species in the oceans, migratory anadromous and freshwater fish and demersal species. SNPs have been used for the identification of species and their hybrids in natural environments, to study the genetic consequences of restocking for conservation purposes and the negative effects on natural populations of fish accidentally escaping from culture. SNPs are very useful for identifying genomic regions correlated with phenotypic variants relevant for wildlife protection, management and aquaculture. Experimental size-selective catches of populations created in tanks have caused evolutionary changes in life cycles of fishes. The research results have been discussed to clarify whether the fish populations in natural conditions can undergo changes due to selective harvesting targeting the fastest-growing fishes.

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Alternatively spliced variants in Atlantic cod (Gadus morhua) support response to variable salinity environment

Cited by 12 publications

References 59 publications

Extensive alternative splicing triggered by mitonuclear mismatch in naturally introgressed Rhinolophus bats

Extensive alternative splicing triggered by mitonuclear mismatch in naturally introgressed Rhinolophus bats

Analysis of Chromosomal Numbers, Mitochondrial Genome, and Full-Length Transcriptome of Onychostoma brevibarba

Single Nucleotide Polymorphism Markers with Applications in Conservation and Exploitation of Aquatic Natural Populations

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