An improved genome assembly for Larimichthys crocea reveals hepcidin gene expansion with diversified regulation and function

Mu, Yinnan; Huo, Jieying; Guan, Yang; Fan, Dingding; Xiao, Xiaoqiang; Wei, Jingguang; Li, Qiuhua; Mu, Pengfei; Ao, Jingqun; Chen, Xinhua

doi:10.1038/s42003-018-0207-3

Cited by 57 publications

(35 citation statements)

References 76 publications

(87 reference statements)

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“…A general theme across several of the analyzed gene families is gene expansions. Gene expansions are recurrent in fish genomes, both within [155,156] and outside [157][158][159] the context of whole-genome duplications. For example, the copy number of immune genes in fish is quite plastic.…”

Section: Gene Expansionsmentioning

confidence: 99%

The round goby genome provides insights into mechanisms that may facilitate biological invasions

et al. 2020

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Background: The invasive benthic round goby (Neogobius melanostomus) is the most successful temperate invasive fish and has spread in aquatic ecosystems on both sides of the Atlantic. Invasive species constitute powerful in situ experimental systems to study fast adaptation and directional selection on short ecological timescales and present promising case studies to understand factors involved the impressive ability of some species to colonize novel environments. We seize the unique opportunity presented by the round goby invasion to study genomic substrates potentially involved in colonization success. Results: We report a highly contiguous long-read-based genome and analyze gene families that we hypothesize to relate to the ability of these fish to deal with novel environments. The analyses provide novel insights from the large evolutionary scale to the small species-specific scale. We describe expansions in specific cytochrome P450 enzymes, a remarkably diverse innate immune system, an ancient duplication in red light vision accompanied by red skin fluorescence, evolutionary patterns of epigenetic regulators, and the presence of osmoregulatory genes that may have contributed to the round goby's capacity to invade cold and salty waters. A recurring theme across all analyzed gene families is gene expansions. Conclusions: The expanded innate immune system of round goby may potentially contribute to its ability to colonize novel areas. Since other gene families also feature copy number expansions in the round goby, and since other Gobiidae also feature fascinating environmental adaptations and are excellent colonizers, further long-read genome approaches across the goby family may reveal whether gene copy number expansions are more generally related to the ability to conquer new habitats in Gobiidae or in fish.

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Section: Gene Expansionsmentioning

confidence: 99%

The round goby genome provides insights into mechanisms that may facilitate biological invasions

et al. 2020

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“…The LcBD2 coding sequence was obtained from the genome database of large yellow croaker (Ao et al, 2015;Mu et al, 2018). Its open reading frame (ORF) was amplified by PCR with the primer set of LcBD2-F1…”

Section: Cloning and Sequence Analysis Of Lcbd2 Cdnamentioning

confidence: 99%

Molecular and functional identification of a β‐defensin homolog in large yellow croaker (Larimichthys crocea)

Chen

et al. 2020

Journal of Fish Diseases

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β-defensin (BD) is a cysteine-rich cationic antibacterial peptide that is active against a wide range of bacteria. Here, a β-defensin homolog (LcBD2) was identified in large yellow croaker (Larimichthys crocea). The open reading frame of LcBD2 contains 195 nucleotides, encoding a protein of 64 amino acids that possesses a typical arrangement of six conserved cysteine residues (C 31 , C 37 , C 41 , C 53 , C 59 and C 60). LcBD2 transcripts were constitutively expressed in all examined tissues and significantly increased in head kidney, spleen and gills by Vibrio alginolyticus. The synthetic LcBD2 peptide imparted antimicrobial effects on both Gram-negative bacteria (V. campbellii, V. parahaemolyticus, V. alginolyticus, V. harveyi and Pseudomonas plecoglossicida) and Gram-positive bacteria (Bacillus subtilis). We also observed that after treatment with synthetic LcBD2 peptide, numerous blisters appeared on the membrane of P. plecoglossicida, which in turn may result in cell membrane breakage and bacterial death. Moreover, the synthetic LcBD2 peptide significantly upregulated the expression levels of TNF-α2, IL-1β and CXCL8_L1 in monocytes/macrophages, while downregulated expression level of IL-10. The LcBD2 peptide also remarkedly enhanced the phagocytosis of monocytes/macrophages. These results indicate that LcBD2 not only protects large yellow croaker against multiple bacterial pathogens but also plays a role in activation of monocytes/macrophages.

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“…The large yellow croaker ( Larimichthys crocea ) is an economically important maricultured fish in China, with the highest annual production among maricultured fish species (Ao et al., 2015). With the rapid development of large yellow croaker farming, the bacterial diseases are becoming more and more serious (Mu et al., 2018). At present, the most serious bacterial disease is visceral white nodules disease (VWND) characterized by white nodules in the internal organs, including spleen, kidney and liver, of infected fish.…”

Section: Introductionmentioning

confidence: 99%

An outbreak of visceral white nodules disease caused by Pseudomonas plecoglossicida at a water temperature of 12°C in cultured large yellow croaker (Larimichthys crocea) in China

Wang

Ren

et al. 2020

Journal of Fish Diseases

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The large yellow croaker (Larimichthys crocea) is an economically important maricultured fish in China, with the highest annual production among maricultured fish species (Ao et al., 2015). With the rapid development of large yellow croaker farming, the bacterial diseases are becoming more and more serious (Mu et al., 2018). At present, the most serious bacterial disease is visceral white nodules disease (VWND) characterized by white nodules in the internal organs, including spleen, kidney and liver, of infected fish. The VWND has caused high mortality in the cage-cultured large yellow croaker, resulting in significant economic losses (Zhang, Zhou, An, Chen, & Wang, 2014). As early as 2002, the VWND was epidemic in cultured large yellow croaker in Fujian, China, with a high mortality rate of about 70%-80% (Liu, Yu, Lin, Chen, & Xie, 2004). The obvious symptoms included many white nodules with a diameter of 1-2 mm observed in spleen, kidney and liver, congestion in mandible and gill cover, and inflammation in intestine. Two Pseudomonas strains (BP-1 and BS-2) were isolated and identified as the aetiological agents of this disease (Liu et al., 2004). In 2005, an outbreak of the VWND occurred in farmed large yellow croaker in Zhejiang, China, and its pathogen was identified as Pseudomonas putida (Shen

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An improved genome assembly for Larimichthys crocea reveals hepcidin gene expansion with diversified regulation and function

Cited by 57 publications

References 76 publications

The round goby genome provides insights into mechanisms that may facilitate biological invasions

The round goby genome provides insights into mechanisms that may facilitate biological invasions

Molecular and functional identification of a β‐defensin homolog in large yellow croaker (Larimichthys crocea)

An outbreak of visceral white nodules disease caused by Pseudomonas plecoglossicida at a water temperature of 12°C in cultured large yellow croaker (Larimichthys crocea) in China

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