High-Quality Genome Assembly and Annotation of the Big-Eye Mandarin Fish (Siniperca knerii)

Abstract

The big-eye mandarin fish (Siniperca knerii) is an endemic species of southern China. It belongs to the family Sinipercidae, which is closely related to the well-known North American sunfish family Centrarchidae. Determining the genome sequence of S. knerii would provide a foundation for better examining its genetic diversity and population history. A novel sequenced genome of the Sinipercidae also would help in comparative study of the Centrarchidae using Siniperca as a reference. Here, we determined the genome sequence of S. knerii using 10x Genomics technology and next-generation sequencing. Paired-end sequencing on a half lane of HiSeq X platform generated 56 Gbp of raw data. Read assembly using Supernova assembler resulted in two haplotype genomes with 732.1 Mb in size and an average GC content of 40.4%, which is consistent with genome size previously reported or estimated using k-mer counting. A total of 7,989 scaffolds with an N50 score of 12.64 Mb were obtained. The longest scaffold was 30.54 Mb. Evaluation of the genome completeness using BUSCO confirmed that 96.5% genes of the Actinopterygii Benchmarking Universal Single-Copy Orthologs were found in the assembled genome of S. knerii. Gene prediction using Maker annotation kit resulted in 28,440 genes, of which 25,899 genes had at least one hit comparing to the NCBI Nr database, KEGG or InterProScan5. Pairwise sequentially Markovian coalescent (PSMC) analysis of the genome showed that there was a bottleneck event of the population of S. knerii between 70 ka – 20 ka, which was concordant with the Tali glacier period, suggesting a population decline of S. knerii probably due to climate conditions.

Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish (Silurus glanis) Using Linked-Read Sequencing

“…2), this is comparable to other genome assemblies generated using only linked-read technology (e.g. Hammond et al 2017;Jones et al 2017;Ozerov et al 2018;Lu et al 2020). In addition, high completeness and accuracy of the presented S. glanis genome assembly was supported by high sequence similarities and concordant alignment with the chromosome regions of I. punctatus (Liu et al 2016;Fig.…”

Inferring the Demographic History of Japanese Eel (Anguilla japonica) from Genomic Data: Insights for Conservation and Fisheries Management

“…Because the PSMC and MSMC methods perform less well for inferences of demographic history within the last 20 ky (Mather et al, 2020), we interpret population size changes after the LGM with caution. However, the results of this study (population growth 14−17 kya), a previous study of Japanese eel (population expansion 9−25 kya; Tseng et al, 2012), and studies of other species (three tropical Anguilla species; Barth et al, 2020), as well as other northwest Pacific fishes (Lu et al, 2020;Xu et al, 2019), all provide evidence for post-LGM population growth, suggesting that oceanic conditions were generally suitable for population expansion at that time. In the case of Japanese eel, perhaps abrupt sea level rise at the end of the LGM (14.5 kya; Clark et al, 2009) and the inundation of the Taiwan−Ryukyu land bridge 10 kya (Ujiié & Ujiié, 1999), which restored the Kuroshio Current to its present-day path, provided an opportunity for geographic population expansion and population size increase.…”

Genome assembly and annotation of the California harvester antPogonomyrmex californicus

“…Supernova was originally designed for de novo assemblies of human genomes ( Weisenfeld et al 2017 ). Nevertheless, recently it has been successfully used for non-human genome assemblies ( Ozerov et al 2018 ; Wang et al 2019 ; Lu et al 2020 ). For human genomes, a 56× coverage is recommended.…”