Genomic Profiling and Genetic Resource Evaluation of Scoliodon macrorhynchos

doi:10.11924/j.issn.1000-6850.casb2025-0473

Abstract

Abstract:

The Pacific spadenose shark (Scoliodon macrorhynchos) is a cartilaginous fish commonly found in China's coastal waters. In recent years, the population resources of this species are continuously declining and it has been listed as Near Threatened on the IUCN Red List. In order to further understand the species and provide a basis for its scientific management and protection, this study investigated and analyzed genomic genetic resources of S. macrorhynchos. In this study, whole-genome resequencing was performed on the genomic DNA of the S. macrorhynchos. Using the resequencing data, preliminary genome assembly was conducted and its quality was evaluated. Genome-wide identification of microsatellite loci was carried out with calculation of their relative abundance. The complete mitochondrial genome sequence was de novo assembled using bioinformatics software. The assembled mitochondrial sequence was comparatively analyzed against published GenBank reference sequences to identify variant sites; variations were annotated by genomic location (protein-coding genes, tRNA genes, and the control region) and analyzed for nonsynonymous substitutions. The results showed that the genome of the S. macrorhynchos exhibited the following characteristics: size= 2991.63 Mb, heterozygosity rate= 0.46%, repetitive sequence proportion= 63.37% and GC content= 44.34%. The preliminary genome assembly yielded a total length of 2482 Mb with a scaffold N₅₀ of 3342 bp. A total of 470542 microsatellite loci were identified genome-wide, with a relative abundance of about 189.58 loci/Mb. The complete mitochondrial genome sequence (16693 bp) was de novo assembled using bioinformatics tools, consistent with published GenBank reference sequences. Comparative analysis revealed 19 variant sites in the mitochondrial genome: 16 in protein-coding genes, 2 in tRNA genes, and 1 in the control region. Among variants in protein-coding genes, 4 were nonsynonymous substitutions located in the COIII, ND4, ND5, and Cyt b genes. The genome of the S. macrorhynchos is likely of a complex type. This study obtained foundational genetic resources including a draft genome assembly, genome-wide microsatellite markers, and mitochondrial genome data. Comparative mitochondrial genome analysis revealed heightened variability in protein-coding regions. Multiple nonsynonymous substitutions detected in key mitochondrial genes (COIII, ND4, ND5, Cyt b) suggest that relaxed purifying selection may be the primary evolutionary driver of the mitochondrial genome in this species. This research aims to provide essential genetic resources for advancing S. macrorhynchos genomics studies, investigations of genetic evolution, and conservation initiatives.

Key words: Scoliodon macrorhynchos, genomic survey analysis, genome assembly, microsatellite loci, complete mitochondrial genome

LIU Xiaoru, LI Mingseng, ZHANG Yaoren, XU Shengyong. Genomic Profiling and Genetic Resource Evaluation of Scoliodon macrorhynchos[J]. Chinese Agricultural Science Bulletin, 2025, 41(28): 139-145.

Figures/Tables 7

References 38

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文库	原始数据/bp	有效率/%	错误率/%	Q₂₀/%	Q₃₀/%	GC含量/%
文库1	51352795200	84.85	0.03	96.19	90.92	43.04
文库2	52587060600	84.77	0.03	96.00	90.33	43.04

文库	原始数据/bp	有效率/%	错误率/%	Q₂₀/%	Q₃₀/%	GC含量/%
文库1	51352795200	84.85	0.03	96.19	90.92	43.04
文库2	52587060600	84.77	0.03	96.00	90.33	43.04

组装水平	全长/bp	总数	最大长度/bp	N₅₀长度/bp
Contig	2459384968	3119882	49092	2759
Scaffold	2482038903	2855390	76040	3342

组装水平	全长/bp	总数	最大长度/bp	N₅₀长度/bp
Contig	2459384968	3119882	49092	2759
Scaffold	2482038903	2855390	76040	3342

基因	变异位点数量	非同义位点数量	同义位点数量
ND1	1	0	1
tRNA-Ile	1	—	—
ND2	3	0	3
COI	1	0	1
ATP6	2	0	2
COIII	2	1	1
ND3	2	0	2
tRNA-Arg	1	—	—
ND4	2	1	1
ND5	2	1	1
Cyt b	1	1	0
CR	1	—	—