The subgenomes show asymmetric expression of alleles in hybrid lineages of <i>Megalobrama amblycephala</i> × <i>Culter alburnus</i>

Ren, Li; Li, Wuhui; Qin, Qinbo; Dai, He; Han, Fengming; Xiao, Jun; Gao, Xin; Cui, Jialin; Wu, Chang; Yan, Xiaojing; Wang, Guoliang; Liu, Guiming; Liu, Jia; Li, Jiaming; Wan, Zhong; Yang, Chungang; Chun, Zhang; Tao, Min; Wang, Jing; Luo, Kun; Wang, Shi; Hu, Fangzhou; Zhao, Rurong; Li, Xuming; Liu, Min; Zheng, Hongkun; Zhou, Rong; Shu, Yuqin; Wang, Yude; Liu, Qinfeng; Tang, Chenchen; Duan, Wei; Liu, Shaojun

doi:10.1101/gr.249805.119

Cited by 60 publications

(39 citation statements)

References 46 publications

(58 reference statements)

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“…In the present study, we also cloned culter mrap2a and mrap2b , and showed that similar to MRAP2s of other species, culter MRAP2a and MRAP2b had one potential N -linked glycosylation site in the N-terminal domain and a single highly conserved TMD ( Figure 2 and Supplementary Figure 3 ). Based on culter genomic data ( 43 ), we did not identify MRAP1 in topmouth culter, consistent with the hypothesis that MRAP1 is lost in lobe-finned fish, amphibians, and reptiles ( 39 , 56 ). The tissue expression data showed that mrap2a and mrap2b were highly expressed in the central nervous system ( Figures 3C–F ), similar to the expression of mc4r , indicates that caMRAP2a or caMRAP2b might modulate MC4R signaling in the central nervous system.…”

Section: Discussionsupporting

confidence: 79%

Regulation of Melanocortin-4 Receptor Pharmacology by Two Isoforms of Melanocortin Receptor Accessory Protein 2 in Topmouth Culter (Culter alburnus)

Tao

Huang

et al. 2020

Front. Endocrinol.

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Melanocortin-4 receptor (MC4R) plays important roles in regulation of multiple physiological processes, and interaction of MC4R and melanocortin receptor accessory protein 2 (MRAP2) is suggested to play pivotal role in energy balance of vertebrates. Topmouth culter (Culter alburnus) is an economically important freshwater fish in China. Herein we cloned culter mc4r, mrap2a, and mrap2b. Culter mc4r consisted of a 981 bp open reading frame encoding a protein of 326 amino acids. qRT-PCR revealed that mc4r, mrap2a, and mrap2b were primarily expressed in the central nervous system. In the periphery, mc4r and mrap2b were expressed more widely in the male, while mrap2a was expressed more widely in the female. Culter MC4R could bind to four peptide agonists and increase intracellular cAMP production dose dependently. Culter MC4R was constitutively active in both cAMP and ERK1/2 pathways, which was differentially regulated by culter MRAP2a and MRAP2b. Culter MRAP2a significantly increased B max and decreased agonist-stimulated cAMP, while MRAP2b increased cell surface and total expression but did not affect B max and agonist-stimulated cAMP. These results will aid the investigation of the potential physiological processes that MC4R might be involved in topmouth culter.

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Section: Discussionsupporting

confidence: 79%

Regulation of Melanocortin-4 Receptor Pharmacology by Two Isoforms of Melanocortin Receptor Accessory Protein 2 in Topmouth Culter (Culter alburnus)

Tao

Huang

et al. 2020

Front. Endocrinol.

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“…This may be explained if trans divergence results from a limited activity of a TF in one of the species, which indeed appears to explain a considerable fraction of trans-effects we observe. This may provide a mechanistic explanation for the phenomenon of genome asymmetry that was reported before in a variety of organisms (Feldman et al, 2012;Lemos et al, 2008;Ren et al, 2019) whereby the phenotypic manifestation of some traits, including gene expression patterns, favors one genome over the other rather than being intermediate.…”

Section: Discussionmentioning

confidence: 57%

Independent evolution of transcript abundance and gene regulatory dynamics

Krieger

Lupo

Levy³

et al. 2020

Preprint

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Changes in gene expression drive novel phenotypes, raising interest in how gene expression evolves. In contrast to the static genome, cells regulate gene expression to accommodate changing conditions. Previous comparative studies focused on specific conditions, describing inter-species variation in expression levels, but providing limited information about variations in gene regulation. To close this gap, we profiled gene expression of related yeast species in hundreds of conditions, and used co-expression analysis to distinguish variations in transcription regulation from variations in expression levels or environmental perception. The majority of genes whose expression varied between the species maintained a conserved transcriptional regulation. Profiling the interspecific hybrid provided insights into the basis of variations, showed that trans-varying alleles interact dominantly, and revealed complementation of cis-variations by variations in trans.Our data suggests that gene expression diverges primarily through changes in promoter strength that do not alter gene positioning within the transcription network.

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“…All available Sox genes were identified in the zebrafish genome 1 . These Sox genes were used to search for their respective BSB and 2nRCC counterparts in the available BSB and 2nRCC genomic resources (project ID: PRJNA481500) using Blast (V2.5.0) software (Chen et al, 2019;Ren et al, 2019). The CDs lengths and aa numbers of the putative Sox genes were identified from the BSB and 2nRCC genomes.…”

Section: Preparation Of Chromosome Spreadsmentioning

confidence: 99%

“…The goldfish (2nRCC, 2n = 100) is raised over all Asia for food and as an ornamental pet (Liu et al, 2016;Chen et al, 2019), while Megalobrama amblycephala (blunt snout bream, 2n = 48, BSB) is an economically important freshwater fish (Ren et al, 2019). In previous studies, we artificially obtained fertile allotetraploids (4nRB, 4n = 148, F 1 ) from the distant hybridization of 2nRCC (♀) × BSB (♂) (Liu et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

Sox Gene Family Revealed Genetic Variations in Autotetraploid Carassius auratus

Huang

Gong

et al. 2020

Front. Genet.

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The Sox gene family encoded transcription factors that played key roles in developmental processes in vertebrates. To further understand the evolutionary fate of the Sox gene family in teleosts, the Sox genes were comprehensively characterized in fish of different ploidy levels, including blunt snout bream (2n = 48, Megalobrama amblycephala, BSB), goldfish (2n = 100, Carassius auratus red var., 2nRCC), and autotetraploid C. auratus (4n = 200, 4nRCC). The 4nRCC, which derived from the whole genome duplication (WGD) of 2nRCC, were obtained through the distant hybridization of 2nRCC (♀) × BSB (♂). Compared with the 26 Sox genes in zebrafish (2n = 50, Danio rerio), 26, 47, and 92 putative Sox genes were identified in the BSB, 2nRCC, and 4nRCC genomes, respectively, and classified into seven subfamilies (B1, B2, C, D, E, F, and K). Comparative analyses showed that 89.36% (42/47) of Sox genes were duplicated in 2nRCC compared with those in BSB, while 97.83% (90/92) of Sox genes were duplicated in 4nRCC compared with those in 2nRCC, meaning the Sox gene family had undergone an expansion in BSB, 2nRCC, and 4nRCC, respectively, following polyploidization events. In addition, potential gene loss, genetic variations, and paternal parent SNP locus insertion occurred during the polyploidization events. Our data provided new insights into the evolution of the Sox gene family in polyploid vertebrates after several rounds of WGD events.

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The subgenomes show asymmetric expression of alleles in hybrid lineages of Megalobrama amblycephala × Culter alburnus

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Cited by 60 publications

References 46 publications

Regulation of Melanocortin-4 Receptor Pharmacology by Two Isoforms of Melanocortin Receptor Accessory Protein 2 in Topmouth Culter (Culter alburnus)

Regulation of Melanocortin-4 Receptor Pharmacology by Two Isoforms of Melanocortin Receptor Accessory Protein 2 in Topmouth Culter (Culter alburnus)

Independent evolution of transcript abundance and gene regulatory dynamics

Sox Gene Family Revealed Genetic Variations in Autotetraploid Carassius auratus

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