The Xiamen Symposium on Marine Environmental Sciences (XMAS 2025)

ID / Created Time

257 / 2024-09-12 21:11:20

Title

Knowledge on hawksbill sea turtle based on the genomics from Naozhou Island Waters in South China Sea

Keywords

Hawksbill turtle,Eretmochelys imbricata,Genome,SNP,D-loop

Track/Subject

Session 72 - Sea turtle and marine mammal conservation: management, academic and outreach perspectives

Status

Abstract Accepted

Author

Zixuan Zhuo / Key Laboratory of Aquaculture of Aquatic and Economic Animals in the South China Sea, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, Guangdong, China.

Zebin Yao / Key Laboratory of Aquaculture of Aquatic and Economic Animals in the South China Sea, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, Guangdong, China.

Jiao Tang / Key Laboratory of Aquaculture of Aquatic and Economic Animals in the South China Sea, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, Guangdong, China.

Ming Li / Key Laboratory of Aquaculture of Aquatic and Economic Animals in the South China Sea, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, Guangdong, China.

Xiuyue Wang / Key Laboratory of Aquaculture of Aquatic and Economic Animals in the South China Sea, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, Guangdong, China.

Jiahao Song / State Key Laboratory of Marine Environmental Science and School of Ocean and Earth Science, Xiamen University, Xiamen 361102, Fujian, China.

Min Liu / State Key Laboratory of Marine Environmental Science and School of Ocean and Earth Science, Xiamen University, Xiamen 361102, Fujian, China.

Yusong Guo / Key Laboratory of Aquaculture of Aquatic and Economic Animals in the South China Sea, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, Guangdong, China.；Key Laboratory of Prevention and Control of Aquatic Animal Diseases and Healthy Aquaculture of Guangdong Province, Zhanjiang 524088, Guangdong, China.

Zhongduo Wang / Key Laboratory of Aquaculture of Aquatic and Economic Animals in the South China Sea, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, Guangdong, China.；Key Laboratory of Prevention and Control of Aquatic Animal Diseases and Healthy Aquaculture of Guangdong Province, Zhanjiang 524088, Guangdong, China.

Abstract

The critically endangered hawksbill turtle (Eretmochelys imbricata) is a species of significant ecological and conservation importance. This study presents a comprehensive genomic analysis of E. imbricata, combining high-quality genome sequencing with population genetics in the South China Sea. We report the first chromosome-level genome assembly for E. imbricata, spanning 2,138.26 Mb with a contig N50 of 123.49 Mb and scaffold N50 of 137.21 Mb. The assembly comprises 28 chromosomes containing 20,206 protein-coding genes, with 99.48% functionally annotated. Comparative genomic analysis revealed an expansion in olfactory receptor genes and positive selection in immune, sensory, and aging-related systems, suggesting adaptations to aquatic environments and longevity. We further investigated the genetic structure of hawksbill turtle populations in Naozhou Island Waters using whole-genome resequencing of 13 individuals. The analysis yielded 337.54 GB of high-quality data with an average sequencing depth of 11x. We identified 12,703,462 SNPs, with 114,273 located in exonic regions. PCA analysis showed no distinct clustering, indicating diverse origins of the sampled individuals. Demographic analysis revealed population fluctuations over the past 50 million years, with a recent sharp decline stabilizing around 1 million years ago. LD analysis indicated high genetic diversity, particularly on chromosomes 1, 13, 14, and 24—annotation of polymorphic sites highlighted olfactory receptor and immunoglobulin heavy chain genes under strong positive selection.

Additionally, we analyzed whole mitochondrial genomes, integrating D-loop data from global samples to provide a comprehensive phylogeographic context. This analysis revealed high genetic diversity (Hd = 0.974, Pi = 0.01477) and identified six known and five private haplotypes. Phylogenetic analysis indicated the presence of two Indo-Pacific lineages and significant gene flow with certain Australian rookeries while showing marked differentiation from Southeast Asian and American populations. This study provides valuable genomic resources for understanding E. imbricata's genetic evolution and highlights the unique genetic composition of the Naozhou Island Waters population. Our findings suggest this population should be considered an independent management unit, emphasizing the need for targeted conservation strategies in the South China Sea region.

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