scholarly journals Transcriptional development of phospholipid and lipoprotein metabolism in different intestinal regions of Atlantic salmon (Salmo salar) fry

2017 ◽  
Author(s):  
Yang Jin ◽  
Rolf Erik Olsen ◽  
Mari-Ann Østensen ◽  
Gareth Benjamin Gillard ◽  
Sven Arild Korsvoll ◽  
...  
Keyword(s):  
Atlantic Salmon ◽  
Salmo Salar ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
De Novo ◽  
Dietary Lipids ◽  
Whole Genome ◽  
Pyloric Caeca ◽  
Homologous Genes ◽  
Salmon Fry

AbstractBackgroundIt has been suggested that the high phospholipid (PL) requirement in Atlantic salmon (Salmo salar) fry is due to insufficient intestinal de-novo synthesis causing low lipoprotein (LP) production and reduced transport capacity of dietary lipids. However, there has not been performed any in-depth ontological analysis of intestinal PL and LP synthesis with development of salmon. Therefore in this paper we used RNA-seq technology to test the hypothesis that the high PL requirement in salmon fry was associated with undeveloped PL synthesis and LP formation pathways in intestine. There was a special focus on the understanding homologous genes, especially from salmonid-specific fourth vertebrate whole-genome duplication (Ss4R), contribution to salmonid specific features of regulation of PL metabolic pathways. The study was performed in stomach, pyloric caeca and hindgut at 0.16g (1 day before first-feeding), 2.5g and 10g of salmon.ResultsIn general, we found an up-regulation of de-novo phosphatidylcholine (PtdCho) synthesis, phosphatidylethanolamine (PtdEtn) and LP formation pathways in pyloric caeca of salmon between 0.16g and 10g. Thirteen genes in these pathways were highly (q<0.05) up-regulated in 2.5g salmon compared to 0.16g, while only five more significant (q<0.05) genes were found when the fish grew up to 10g. Different homologous genes were found dominating in stomach, pyloric caeca and hindgut. However, the expression of dominating genes in PL and LP synthesis pathways was much higher in pyloric caeca than stomach and hindgut. Salmon-specific homologous (Ss4R) genes had similar expression during development, while other homologs had more diverged expression.ConclusionsAn increasing capacity for PL synthesis and LP formation was confirmed in pyloric caeca. The up-regulation of the de-novo PtdCho pathway confirms that the salmon fry have increasing requirement for dietary PtdCho compared to adult. The similar expressions between Ss4R homologous genes suggest that the functional divergence of these genes was incomplete compared to homologs derived from other whole genome duplication. The results of the present study have provided new information on the molecular mechanisms of phospholipid synthesis and lipoprotein formation in fish.

scholarly journals The grayling genome reveals selection on gene expression regulation after whole genome duplication

2017 ◽  
Author(s):  
Srinidhi Varadharajan ◽  
Simen R. Sandve ◽  
Gareth B. Gillard ◽  
Ole K. Tørresen ◽  
Teshome D. Mulugeta ◽  
...  
Keyword(s):  
Atlantic Salmon ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Draft Genome ◽  
Tissue Expression ◽  
Expression Regulation ◽  
Niche Shift ◽  
Whole Genome ◽  
Expression Divergence ◽  
European Grayling

AbstractWhole genome duplication (WGD) has been a major evolutionary driver of increased genomic complexity in vertebrates. One such event occurred in the salmonid family ~80 million years ago (Ss4R) giving rise to a plethora of structural and regulatory duplicate-driven divergence, making salmonids an exemplary system to investigate the evolutionary consequences of WGD. Here, we present a draft genome assembly of European grayling (Thymallus thymallus) and use this in a comparative framework to study evolution of gene regulation following WGD. Among the Ss4R duplicates identified in European grayling and Atlantic salmon (Salmo salar), one third reflect non-neutral tissue expression evolution, with strong purifying selection, maintained over ~50 million years. Of these, the majority reflect conserved tissue regulation under strong selective constraints related to brain and neural-related functions, as well as higher-order protein-protein interactions. A small subset of the duplicates has evolved tissue regulatory expression divergence in a common ancestor, which have been subsequently conserved in both lineages, suggestive of adaptive divergence following WGD. These candidates for adaptive tissue expression divergence have elevated rates of protein coding- and promoter-sequence evolution and are enriched for immune- and lipid metabolism ontology terms. Lastly, lineage-specific duplicate divergence points towards underlying differences in adaptive pressures on expression regulation in the non-anadromous grayling versus the anadromous Atlantic salmon.Our findings enhance our understanding of the role of WGD in genome evolution and highlights cases of regulatory divergence of Ss4R duplicates, possibly related to a niche shift in early salmonid evolution.

scholarly journals Regulatory divergence of homeologous Atlantic salmon elovl5 genes following the salmonid-specific whole-genome duplication

Gene ◽  
2016 ◽  
Vol 591 (1) ◽  
pp. 34-42 ◽  
Author(s):  
Greta Carmona-Antoñanzas ◽  
Xiaozhong Zheng ◽  
Douglas R. Tocher ◽  
Michael J. Leaver
Keyword(s):  
Atlantic Salmon ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Whole Genome

scholarly journals De Novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole genome duplication

2018 ◽  
Author(s):  
Zelin Chen ◽  
Yoshihiro Omori ◽  
Sergey Koren ◽  
Takuya Shirokiya ◽  
Takuo Kuroda ◽  
...  
Keyword(s):  
Carassius Auratus ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
De Novo ◽  
Close Relative ◽  
Whole Genome ◽  
Draft Sequence ◽  
Zebrafish Model ◽  
Goldfish Carassius Auratus ◽  
The Common

SummaryFor over a thousand years throughout Asia, the common goldfish (Carassius auratus) was raised for both food and as an ornamental pet. Selective breeding over more than 500 years has created a wide array of body and pigmentation variation particularly valued by ornamental fish enthusiasts. As a very close relative of the common carp (Cyprinus carpio), goldfish shares the recent genome duplication that occurred approximately 14-16 million years ago (mya) in their common ancestor. The combination of centuries of breeding and a wide array of interesting body morphologies is an exciting opportunity to link genotype to phenotype as well as understanding the dynamics of genome evolution and speciation. Here we generated a high-quality draft sequence of a “Wakin” goldfish using 71X PacBio long-reads. We identified 70,324 coding genes and more than 11,000 non-coding transcripts. We found that the two sub-genomes in goldfish retained extensive synteny and collinearity between goldfish and zebrafish. However, “ohnologous” genes were lost quickly after the carp whole-genome duplication, and the expression of 30% of the retained duplicated gene diverged significantly across seven tissues sampled. Loss of sequence identity and/or exons determined the divergence of the expression across all tissues, while loss of conserved, non-coding elements determined expression variance between different tissues. This draft assembly also provides an important resource for comparative genomics with the very commonly used zebrafish model (Danio rerio), and for understanding the underlying genetic causes of goldfish variants.

scholarly journals Chromosome-scale genome assembly of Japanese pear (Pyrus pyrifolia) variety ‘Nijisseiki’

2020 ◽  
Author(s):  
Kenta Shirasawa ◽  
Akihiro Itai ◽  
Sachiko Isobe
Keyword(s):  
Related Species ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
De Novo ◽  
Genetic Maps ◽  
Japanese Pear ◽  
Pyrus Pyrifolia ◽  
Whole Genome ◽  
Protein Encoding ◽  
History Of

AbstractAimThe Japanese pear (P. pyrifolia) variety ‘Nijisseiki’ is valued for its superior flesh texture, which has led to its use as a breeding parent for most Japanese pear cultivars. However, in the absence of genomic resources for Japanese pear, the parents of the ‘Nijisseiki’ cultivar remain unknown, as does the genetic basis of its favorable texture. The genomes of pear and related species are complex due to ancestral whole genome duplication and high heterozygosity, and long-sequencing technology was used to address this.Methods and ResultsDe novo assembly of long sequence reads covered 136× of the Japanese pear genome and generated 503.9 Mb contigs consisting of 114 sequences with an N50 value of 7.6□Mb. Contigs were assigned to Japanese pear genetic maps to establish 17 chromosome-scale sequences. In total, 44,876 protein-encoding genes were predicted, 84.3% of which were supported by predicted genes and transcriptome data from Japanese pear relatives. As expected, evidence of whole genome duplication was observed, consistent with related species.Conclusion and PerspectiveThis is the first genome sequence analysis reported for Japanese pear, and this resource will support breeding programs and provide new insights into the physiology and evolutionary history of Japanese pear.

scholarly journals Genetic drift dominates genome-wide regulatory evolution following an ancient whole genome duplication in Atlantic salmon

2020 ◽  
Author(s):  
Jukka-Pekka Verta ◽  
Henry Barton ◽  
Victoria Pritchard ◽  
Craig Primmer
Keyword(s):  
Atlantic Salmon ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Regulatory Elements ◽  
Functional Redundancy ◽  
Neutral Evolution ◽  
Whole Genome ◽  
Regulatory Evolution ◽  
Whole Genome Duplications ◽  
Genome Duplications

AbstractWhole genome duplications (WGD) have been considered as springboards that potentiate lineage diversification through increasing functional redundancy. Divergence in gene regulatory elements is a central mechanism for evolutionary diversification, yet the patterns and processes governing regulatory divergence following events that lead to massive functional redundancy, such as WGD, remain largely unknown. We studied the patterns of divergence and strength of natural selection on regulatory elements in the Atlantic salmon (Salmo salar) genome, which has undergone WGD 100-80 Mya. Using ChIPmentation, we first show that H3K27ac, a histone modification typical to enhancers and promoters, is associated with genic regions, tissue specific transcription factor binding motifs, and with gene transcription levels in immature testes. Divergence in transcription between duplicated genes from WGD (ohnologs) correlated with difference in the number of proximal regulatory elements, but not with promoter elements, suggesting that functional divergence between ohnologs after WGD is mainly driven by enhancers. By comparing H3K27ac regions between duplicated genome blocks, we further show that a longer polyploid state post-WGD has constrained asymmetric regulatory evolution. Patterns of genetic diversity across natural populations inferred from re-sequencing indicate that recent evolutionary pressures on H3K27ac regions are dominated by largely neutral evolution. In sum, our results suggest that post-WGD functional redundancy in regulatory elements continues to have an impact on the evolution of the salmon genome, promoting largely neutral evolution of regulatory elements despite their association with transcription levels. These results highlight a case where genome-wide regulatory evolution following an ancient WGD is dominated by genetic drift.Significance statementRegulatory evolution following whole genome duplications (WGD) has been investigated at the gene expression level, but studies of the regulatory elements that control expression have been lacking. By investigating regulatory elements in the Atlantic salmon genome, which has undergone a whole genome duplication 100-80 million years ago, we discovered patterns suggesting that neutral divergence is the prevalent mode of regulatory element evolution post-WGD. Our results suggest mechanisms for explaining the prevalence of asymmetric gene expression evolution following whole genome duplication, as well as the mismatch between evolutionary rates in enhancers versus that of promoters.

scholarly journals De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication

2019 ◽  
Vol 5 (6) ◽  
pp. eaav0547 ◽  
Author(s):  
Zelin Chen ◽  
Yoshihiro Omori ◽  
Sergey Koren ◽  
Takuya Shirokiya ◽  
Takuo Kuroda ◽  
...  
Keyword(s):  
Carassius Auratus ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
De Novo ◽  
Close Relative ◽  
Whole Genome ◽  
Draft Sequence ◽  
Goldfish Carassius Auratus ◽  
The Common ◽  
Conserved Noncoding Elements

For over a thousand years, the common goldfish (Carassius auratus) was raised throughout Asia for food and as an ornamental pet. As a very close relative of the common carp (Cyprinus carpio), goldfish share the recent genome duplication that occurred approximately 14 million years ago in their common ancestor. The combination of centuries of breeding and a wide array of interesting body morphologies provides an exciting opportunity to link genotype to phenotype and to understand the dynamics of genome evolution and speciation. We generated a high-quality draft sequence and gene annotations of a “Wakin” goldfish using 71X PacBio long reads. The two subgenomes in goldfish retained extensive synteny and collinearity between goldfish and zebrafish. However, genes were lost quickly after the carp whole-genome duplication, and the expression of 30% of the retained duplicated gene diverged substantially across seven tissues sampled. Loss of sequence identity and/or exons determined the divergence of the expression levels across all tissues, while loss of conserved noncoding elements determined expression variance between different tissues. This assembly provides an important resource for comparative genomics and understanding the causes of goldfish variants.

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