scholarly journals Updated Genome Assembly of Bighead Carp (Hypophthalmichthys nobilis) and Its Differences Between Male and Female on Genomic, Transcriptomic, and Methylation Level

2021 ◽  
Vol 12 ◽  
Author(s):  
Beide Fu ◽  
Ying Zhou ◽  
Haiyang Liu ◽  
Xiaomu Yu ◽  
Jingou Tong

Cyprinidae is one of the largest family in freshwater fishes, and it is most intensively cultured fish taxon of the world. However, studies about sex determination in this large family is still rear, and one of the reasons is lack of high quality and complete genome. Here, we used nanopore to sequence the genome of a male bighead carp, obtaining contig N50 = 24.25 Mb, which is one of the best assemblies in Cyprinidae. Five males and five females were re-sequenced, and a male-specific region on LG19 was confirmed. We find this region holds many male-specific markers in other Cyprinidae fishes, such as grass carp and silver carp. Transcriptome analyses of hypothalamus and pituitary tissues showed that several sex-specific differentially expressed genes were associated with steroid biosynthesis. The UCH64E gene, located in the male-specific region on LG19, showed higher expression levels in male than female tissues of bighead carp. The methyl-RAD of hypothalamus tissues between males and females indicated that the sexual methylation differences are significant in bighead carp. We also compared the methylation sites recognized using methyl-RAD and nanopore raw reads and found that approximately 73% of the methylation sites identified using methyl-RAD were within nanopore CpG sites.

<em>Abstract</em>.—Bighead Carp <em>Hypophthalmichthys nobilis </em>and Silver Carp <em>H. molitrix </em>are native in the Yangtze River and extremely important economically and culturally as food fishes; however, the two species have declined due to overfishing and anthropogenic modifications to hydrology and water quality. Bighead Carp and Silver Carp were imported to North America in the early 1970s, escaped confinement, and have now become undesirable and problematic invasive species. The two carps have become the most abundant fish species in many portions of their invaded range, which continues to expand. We compare the biology, status, and management of these species between their natal range in the Yangtze River and their invaded habitats of the Mississippi River basin.


2017 ◽  
Vol 26 (5) ◽  
pp. 1165-1171 ◽  
Author(s):  
Hadiseh Dadras ◽  
Amin Golpour ◽  
Mehri Zahmatkesh ◽  
Hossein Khara ◽  
Shahrouz Baradaran Noveiri ◽  
...  

2020 ◽  
Vol 71 (7) ◽  
pp. 761
Author(s):  
Chaoqun Su ◽  
Wenjing Hu ◽  
Zhongjun Hu ◽  
Zhen Zhang ◽  
Oranich Wedchaparn ◽  
...  

High-throughput sequencing analysis of gut contents was used to study the feeding habits of two filter-feeding fish, namely silver carp Hypophthalmichthys molitrix and bighead carp Hypophthalmichthys nobilis, in mesotrophic Lake Qiandao and eutrophic Lake Taihu. Silver carp feed primarily on phytoplankton, with a feeding preference for Chlorophyta, in Lake Qiandao and rely on phytoplankton in Lake Taihu. Bighead carp feed more on zooplankton in Lake Qiandao and on phytoplankton in Lake Taihu. With increasing levels of algae, bighead carp feed more on phytoplankton. The dietary shifts suggest that bighead carp would be useful in controlling nuisance algae in lakes.


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