Chromosome‐Level Genome Assembly for the Largemouth Bass
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Received: 1 April 2020 | Revised: 19 August 2020 | Accepted: 24 August 2020 DOI: 10.1111/1755-0998.13256 RESOURCE ARTICLE Chromosome-level genome assembly for the largemouth bass Micropterus salmoides provides insights into adaptation to fresh and brackish water Chengfei Sun1 | Jia Li2 | Junjian Dong1 | Yongchao Niu3 | Jie Hu1 | Jinmin Lian3 | Wuhui Li1 | Jiang Li3 | Yuanyuan Tian1 | Qiong Shi2 | Xing Ye1 1Key Laboratory of Tropical and Subtropical Fishery Resource Application and Abstract Cultivation, Ministry of Agriculture and Largemouth bass (LMB; Micropterus salmoides) has been an economically important Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery fish in North America, Europe, and China. This study obtained a chromosome-level Sciences, Guangzhou, China genome assembly of LMB using PacBio and Hi-C sequencing. The final assem- 2 Shenzhen Key Laboratory of Marine bled genome is 964 Mb, with contig N50 and scaffold N50 values of 1.23 Mb and Genomics, Guangdong Provincial Key Laboratory of Molecular Breeding in Marine 36.48 Mb, respectively. Combining with RNA sequencing data, we annotated a total Economic Animals, BGI Academy of Marine of 23,701 genes. Chromosomal assembly and syntenic analysis proved that, unlike Sciences, BGI Marine, BGI, Shenzhen, China 3Biozeron Shenzhen Inc., Shenzhen, China most Perciformes with the popular haploid chromosome number of 24, LMB has only 23 chromosomes (Chr), among which the Chr1 seems to be resulted from a chro- Correspondence Xing Ye, Key Laboratory of Tropical and mosomal fusion event. LMB is phylogenetically closely related to European seabass Subtropical Fishery Resource Application and spotted seabass, diverging 64.1 million years ago (mya) from the two seabass and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research species. Eight gene families comprising 294 genes associated with ionic regulation Institute, Chinese Academy of Fishery were identified through positive selection, transcriptome and genome comparisons. Sciences, Guangzhou, China. Email: [email protected] These genes involved in iron facilitated diffusion (such as claudin, aquaporins, so- dium channel protein and so on) and others related to ion active transport (such as Qiong Shi, Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial sodium/potassium-transporting ATPase and sodium/calcium exchanger). The claudin Key Laboratory of Molecular Breeding in gene family, which is critical for regulating cell tight junctions and osmotic homeo- Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, stasis, showed a significant expansion in LMB with 27 family members and 68 copies Shenzhen, China. for salinity adaptation. In summary, we reported the first high-quality LMB genome, Email: [email protected] and provided insights into the molecular mechanisms of LMB adaptation to fresh and Funding information brackish water. The chromosome-level LMB genome will also be a valuable genomic Special Fund for Scientific Research in Public Welfare and Capacity Building of resource for in-depth biological and evolutionary studies, germplasm conservation Guangdong Province, Grant/Award Number: and genetic breeding of LMB. 2017A030303002; Central Public-interest Scientific Institution Basal Research Fund of the Chines Academy of Fishery Sciences, KEYWORDS Grant/Award Number: 2017HY-XKQ0208; chromosomal fusion, chromosome-level genome, ion transport, largemouth bass (Micropterus Youth Program of National Natural Science salmoides), salinity adaptation Foundation of China, Grant/Award Number: 31902354; China Agriculture Research System, Grant/Award Number: CARS-46; Central Public-interest Scientific Institution Basal Research Fund，CAFS, Grant/Award Number: 2020TD23 Chengfei Sun, Jia Li and Junjian Dong contributed equally to this work. Mol Ecol Resour. 2021;21:301–315. wileyonlinelibrary.com/journal/men © 2020 John Wiley & Sons Ltd | 301 302 | SUN ET AL. 1 | INTRODUCTION three-spined stickleback Gasterosteus aculeatus [Jones et al., 2012]) are euryhaline fishes that can adapt to fresh, brackish, and seawa- Largemouth bass (LMB; Micropterus salmoides; order Perciformes, ter habitats (Hirai et al., 1999; Tine et al., 2014). European seabass suborder Percoidei, family Centrarchidae) is one of the most popular can even tolerate up to 60‰ salinity (Jensen et al., 1998; Varsamos game fishes in North America. It is often considered a freshwater fish. et al., 2002). Euryhaline fishes exhibit unique and complex osmo- However, this species is distributed not only in freshwater habitats regulatory functions, whereby the water-ion balance in the body is of North America from central and eastern USA to northern Mexico, maintained via osmoregulatory organs (such as gills, kidneys, and gas- but also in the brackish water and freshwater habitats affected by trointestinal tracts) to adapt to environmental salinity fluctuations tides along the Atlantic coasts of North America and the Gulf of (Boutet et al., 2006; Forsyth & Wallis, 2002; Hirai et al., 1999). The Mexico (Bailey et al., 1954; DeVries et al., 2015; Glover et al., 2012). complex and ever-changing chemical environment in coastal water Most freshwater fishes are hardly adaptable to salinities higher than due to salinity fluctuations is an arduous challenge for freshwater 10‰ (Peterson & Meador, 1994), but LMB exhibits a relatively high fishes like LMB. However, previous studies have shown that LMB liv- salinity tolerance. LMB is often caught in coastal marshes with 1‰– ing in coastal waters, like their inland counterparts with high location 12‰ salinity and in coastal waters with 16‰ salinity. Furthermore, loyalty and do not exhibit large-scale migrations from their original LMB can even be found in aquatic environments with up to 24‰ habitats in response to increased salinity, indicating that LMB can salinity (Bailey et al., 1954; Meador & Kelso, 1990; Page, 2008; tolerate certain levels of salinity and the related physiological effects Peterson & Ross, 1991; Renfro, 1959; Susanto & Peterson, 1996). (Bain & Boltz, 1992; Copeland & Noble, 1994; DeVries et al., 2015; LMB is particularly abundant and has been an important support Glover et al., 2012). In the present study, PacBio and Hi-C sequenc- of the recreational fishing industry in oligohaline areas of estuar- ing techniques were applied to obtain a chromosome-level genome ies throughout the USA Atlantic and Gulf of Mexico coasts (Bailey for LMB, and its evolutionary relationships with other fishes partic- et al., 1954; Glover et al., 2012; Guier et al., 1978; Nack et al., 1993). ularly spotted seabass, European seabass, and Asian seabass, were It has been widely translocated for many decades as a game fish and elucidated via comparative genome analysis. Furthermore, LMB was also as part of large-scale stocking efforts, making it a cosmopolitan exposed to various salinity treatments to compare the transcriptome species (Barthel et al., 2010; Carpenter & Kitchell, 1996). The aqua- changes between fresh and brackish water. Based on the results of culture industries in China, Italy, and Mexico produce approximately comparative genomics and transcriptome analysis, we explored the 458,503 tons of LMB per year (FAO, 2017). Therefore, LMB has be- molecular mechanism of the brackish water adaptation of LMB. Our come an important freshwater aquaculture fish in addition to being a data may provide important resources for extensive studies on ger- popular game fish, with ecological and economic significance. mplasm conservation, mapping of traits with economic importance, High-throughput sequencing has been used to obtain genome and genetic improvements, as well as facilitate in-depth understand- sequences of various fishes, with great significance in clarifying bi- ing of the adaptive mechanisms of freshwater fishes in ecological ological characteristics, evolutionary history, and genetic basis of environments of brackish water. important traits (Bian et al., 2019; Ravi & Venkatesh, 2018). PacBio, a third-generation sequencing technology, and the high-through- put chromosome conformation capture (Hi-C)-assisted genome 2 | MATERIALS AND METHODS assembly technique have recently been applied to obtain chromo- some-level genome assemblies for many economically important 2.1 | Ethics approval and consent to participate fishes, such as spotted seabass (Lateolabrax maculatus), giant grou- per (Epinephelus lanceolatus), Atlantic herring (Clupea harengus), and All the experiments on fishes were conducted in accordance with Alpine whitefish (Coregonus sp.) (Dekayne et al., 2020; Pettersson the specific guidelines on the care and use of animals for scien- et al., 2019; Shao et al., 2018; Zhou et al., 2019), and coral reef fishes, tific purposes as outlined by the Institutional Animal Care and Use such as barred knifejaw (Oplegnathus fasciatus), orange clownfish Committee (IACUC) of the Pearl River Fisheries Institute, Chinese (Amphiprion percula), and Triplophysa tibetana (Lehmann et al., 2019; Academy of Fishery Sciences (CAFS), China. The IACUC approved Xiao et al., 2019; Yang et al., 2019). High-quality genome sequences this study under the CAFS project “Breeding of LMB-2019”. are of great significance for analysing the evolutionary history, sex-determination mechanisms, and genetic mechanisms for fish growth and immunity, as well as the adaptability of fishes living in 2.2 | Genomic DNA extraction and unique habitats, such as coral reefs and extreme environments