The draft genome of blunt snout bream (<i>Megalobrama amblycephala</i>) reveals the development of intermuscular bone and adaptation to herbivorous diet

Han, Lei; Chen, Chunhai; Gao, Zexia; Jiang, Min; Gu, Yongming; Jian, Jianbo; Jiang, Xiewu; Cai, Huimin; Ebersberger, Ingo; Xu, Meng; Zhang, Xinhui; Chen, Jianwei; Luo, Wei; Chen, Boxiang; Chen, Junhui; Liu, Hong; Jiang, Li; Lai, Ruifang; Bai, Mingzhou; Jin, Wei; Yi, Shaokui; Wang, Huanling; Cao, Xiaojuan; Zhou, Xiaoyun; Zhao, Ying‐Zheng; Wei, Kai-Jian; Yang, Ruibin; Liu, Bingnan; Zhao, Shancen; Fang, Xiaodong; Schartl, Manfred; Qian, Xueqiao; Wang, Weimin

doi:10.1093/gigascience/gix039

Cited by 88 publications

(59 citation statements)

References 88 publications

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“…The GC percentage (36%) found in this study is similar to that of the genomes of other cyprinids ( Supplementary Table 6). The overall percentage of repeat elements observed was similar to the repeat contents of the cavefish Sinocyclocheilus grahami (Yang et al, 2016) and grass carp Ctenopharyngodon idellus (Wang et al, 2015), higher than common carp Cyprinus carpio (Xu P. et al, 2014) and blunt snout bream Megalobrama amblycephala (Liu et al, 2017) but lower than zebrafish Danio rerio (Howe et al, 2013) (Supplementary Table 6). The most abundant repeat elements in the rohu genome were found to be DNA transposons, accounting for 33.58% of the classified elements, followed by retrotransposons (6.1%), LINEs (3.5%), and SINEs (0.8%), as observed in other carp genomes.…”

Section: Genome Organizationsupporting

confidence: 62%

De novo Assembly and Genome-Wide SNP Discovery in Rohu Carp, Labeo rohita

et al. 2020

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Section: Genome Organizationsupporting

confidence: 62%

De novo Assembly and Genome-Wide SNP Discovery in Rohu Carp, Labeo rohita

et al. 2020

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“…Duplication of T1R2 genes of stickleback, resulting in enhanced perception for substances important for survival and reproduction, has been suggested as an adaptive strategy to varied environment [28]. In the present study, we observed that high T1R2 duplications in grass carp (six copies) as well as blunt snout bream are related to the vegetarian adaptation through the comparative analysis in cyprinid evolution [29].…”

Section: Discussionsupporting

confidence: 53%

Expansion of sweet taste receptor genes in grass carp (Ctenopharyngodon idellus) coincided with vegetarian adaptation

Yuan

Liang

Cai

et al. 2019

Preprint

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Background: Taste is fundamental to diet selection in vertebrates. Genetic basis of sweet taste receptor in the shaping of food habits has been extensively studied in mammals and birds, but scarcely studied in fishes. Grass carp is an excellent model for studying vegetarian adaptation, as it exhibits food habit transition from carnivory to herbivory. Results: We identified six sweet taste receptors (gcT1R2A-F) in grass carp. The four gcT1R2s (gcT1R2C-F) have been suggested to be evolved from and paralogous to the two original gcT1R2s (gcT1R2A and gcT1R2B). All gcT1R2s were expressed in taste organs and mediated glucose-, fructose- or arginine-induced intracellular calcium signaling, revealing they were functional. In addition, grass carp was performed to prefer fructose to glucose under a behavioral experiment. Parallelly, compared with gcT1R2A-F/gcT1R3 co-transfected cells, gcT1R2C-F/gcT1R3 co-transfected cells showed a higher response to plant-specific fructose. Moreover, food habit transition from carnivory to herbivory in grass carp was accompanied by increased gene expression of certain gcT1R2s. Conclusions: We suggested that the gene expansion of T1R2s in grass carp was an adaptive strategy to accommodate the change in food environment. Moreover, the selected gene expression of gcT1R2s might drive the food habit transition from carnivory to herbivory in grass carp. This study provided some evolutional and physiological clues for the formation of herbivory in grass carp.

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“…The high-quality reads were BLAST searched against the CC genome and BSB genome by applying BWA software with default options (Li and Durbin, 2009). For the genome comparison of RCC-L and GF-L, the RCC-L and the GF-L genome sequences were modelled as sequencing data with 90× read depth and aligned to the CC, BSB, and RCC genomes (Xu et al, 2014;Liu et al, 2016;Liu et al, 2017).…”

Section: Mapping and Identities Using Genome Resequencingmentioning

confidence: 99%

The Hybrid Genome of a New Goldfish-Like Fish Lineage Provides Insights Into the Origin of the Goldfish

et al. 2020

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Distant hybridization leads to obvious changes in genotypes and phenotypes, giving rise to species with novel capabilities. However, the fusion of distinct genomes also polymerizes the DNA or gene variations that occur during the course of evolution. Knowledge of the early stages of post-hybridization evolution is particularly important. Here, we investigated the full-length (FL) transcriptomes and the sequences resulting from the genome resequencing of the red crucian carp-like homodiploid fish (RCC-L) and goldfish-like homodiploid fish (GF-L) derived from the interspecific hybridization of koi carp (KOC) and blunt snout bream (BSB) to provide molecular evidence for the hybrid origin of the goldfish (GF). We compared the orthologous genes in the transcriptomes of RCC-L and GF-L with those of KOC and BSB. We also mapped the orthologous genes to the common carp (CC) and BSB genomes and classified them into eight gene patterns in three categories (chimaera, mutant, and biparental origin genes). The results showed that 48.20% and 46.50% of the genes were chimaera and that 3.70% and 8.30% of the genes were mutations of orthologous genes in RCC-L and GF-L, respectively. In RCC-L and GF-L, 63.70% and 68.20% of the genetic materials were from KOC, and 12.30% and 11.90% of the genetic materials were from BSB. The sequences from the genome resequencing of RCC-L and GF-L were mapped to the genome sequences of CC and BSB, revealing that the similarities of both RCC-L and GF-L to the CC genome (92.52%, 90.18%) were obviously higher than to the BSB genome (50.33%, 49.18%), supporting the suggestion that the genomes of both RCC-L and GF-L were mainly inherited from KOC but had some DNA fragments from BSB. Overall, our results provide molecular biological evidence for the hybrid origin of red crucian carp (RCC) and GF.

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The draft genome of blunt snout bream (Megalobrama amblycephala) reveals the development of intermuscular bone and adaptation to herbivorous diet

Cited by 88 publications

References 88 publications

De novo Assembly and Genome-Wide SNP Discovery in Rohu Carp, Labeo rohita

De novo Assembly and Genome-Wide SNP Discovery in Rohu Carp, Labeo rohita

Expansion of sweet taste receptor genes in grass carp (Ctenopharyngodon idellus) coincided with vegetarian adaptation

The Hybrid Genome of a New Goldfish-Like Fish Lineage Provides Insights Into the Origin of the Goldfish

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