Shuli Zhu

Common carp (Cyprinus carpio) is an important valuable cyprinid in China and has been a popular cultured aquaculture species around the globe. Understanding the genetic diversity of wild native common carp not only provides basic data for the protection and utilisation of common carp resources but also assesses the effect of human activities on the genetic diversity of this species. In this study, genetic diversity and population structure of the common carp from 15 sampling populations in the Pearl River and Nandujiang River were determined using a coalescent mitochondrial locus (MLS), including mitochondrial cytochrome b gene (Cytb) and a control region (D‐loop) segment. The haplotype diversity and nucleotide diversity were 0.962 and 0.00628 in the Pearl River and 0.808 and 0.00376 in the Nandujiang River, respectively. Phylogenetic and haplotype network analyses indicated that three sub‐species (a) C. c. rubrofuscus, (b) C. c. haematopterus and (c) C. c. carpio all occur in both rivers. AMOVA revealed that the variation within populations (86.2%) was the main source of the total variation. Statistically significant genetic differentiation among different Pearl River populations of C. c. rubrofuscus (F_st = 0.05–0.25) and relatively high genetic differentiation between the Nandujiang River population and the Pearl River populations (F_st > 0.238) are apparent. Bayesian clustering analyses detected that global populations consisted of eight genetic clusters and examined that Nandujiang River population included relatively pure genetic clusters. Neutrality tests suggested that native populations experienced recent population expansion, and Extended Bayesian Skyline Plot indicated that the common carp populations likely experienced a historical expansion during 0.125–0.250 MYA. Artificial fish propagation and release, escape from fish farms and Fang Sheng may explain the invasion of non‐native sub‐species in many river sections, such as Laibin, Rongjiang, Huizhou, Heyuan and Zhaoqing. To conserve the native common carp populations, release station should be established to culture native common carp fry. Overall, the findings can be contributed to complementing scientific knowledge for conservation and management of the wild native common carp.

This study aimed to determine the age, growth, mortality, and population structure of the economically important cyprinid silver carpHypophthalmichthys molitrix(Valenciennes, 1844) in the middle and lower reaches of the Pearl River. A total of 297 silver carp were sampled quarterly from the catches of gillnet fishermen, at six sites, between June 2019 and September 2020. Standard length of the specimens ranged from 130 to 585 mm, and body weight ranged from 45.5 to 3930 g. The length–weight relationship parameterbvalues reached 3.015. Age was determined through examination and measurements of fish scales, and the age composition of the sampled silver carp varied from 0+ to 4+. Fitting the new data to the von Bertalanffy growth model, we obtained an asymptotic size (L_∞) of 1107 mm,kof 0.135, andt₀of −0.666 for silver carp in this stretch of the river. The calculated growth performance indexϕand estimated longevityt_maxwere 5.22 and 21.56, respectively. The rates of total mortality, natural mortality, and fishing mortality were calculated as 0.4997, 0.1621, and 0.3377, respectively, while the exploitation ratio was evaluated as 0.6757. The overall results confirm overexploitation of this resource in the middle and lower reaches of the Pearl River. It was concluded that this species should be protected from capture until at least 790 mm in standard length, representing an optimal minimum size for capture to benefit conservation of the species and to sustainably develop this valuable fishery.

Genome complexity such as heterozygosity may heavily influence its de novo assembly. Sequencing somatic cells of the F1 hybrids harboring two sets of genetic materials from both of the paternal and maternal species may avoid alleles discrimination during assembly. However, the feasibility of this strategy needs further assessments. We sequenced and assembled the genome of an F1 hybrid between Silurus asotus and S. meridionalis using the SequelII platform and Hi-C scaffolding technologies. More than 300 Gb raw data were generated, and the final assembly obtained 2344 scaffolds composed of 3017 contigs. The N50 length of scaffolds and contigs was 28.55 Mb and 7.49 Mb, respectively. Based on the mapping results of short reads generated for the paternal and maternal species, each of the 29 chromosomes originating from S. asotus and S. meridionalis was recognized. We recovered nearly 94% and 96% of the total length of S. asotus and S. meridionalis. BUSCO assessments and mapping analyses suggested that both genomes had high completeness and accuracy. Further analyses demonstrated the high collinearity between S. asotus, S. meridionalis, and the related Pelteobagrus fulvidraco. Comparison of the two genomes with that assembled only using the short reads from non-hybrid parental species detected a small portion of sequences that may be incorrectly assigned to the different species. We supposed that at least part of these situations may have resulted from mitotic recombination. The strategy of sequencing the F1 hybrid genome can recover the vast majority of the parental genomes and may improve the assembly of complex genomes.

?й?ˮ????ѧ??????ͨ???ڿ????߱༭ϵͳ??????Ͷ??