Blood Transcriptome Analysis Reveals Gene Expression Differences between Yangtze Finless Porpoises from Two Habitats: Natural and Ex Situ Protected Waters

Comparative Blood Transcriptome Analysis of Semi-Natural and Controlled Environment Populations of Yangtze Finless Porpoise

The Yangtze finless porpoises (Neophocaena asiaeorientalis asiaeorientalis) living in different environments display significant differences in behavior and physiology. To compare and analyze gene expression differences between an ex situ population and a controlled environment population of the Yangtze finless porpoise, we sequenced the transcriptome of blood tissues living in a semi-natural reserve and an artificial facility, respectively. We identified 6860 differentially expressed genes (DEGs), of which 6603 were up-regulated and 257 were down-regulated in the controlled environment vs ex situ comparison. GO and KEGG enrichment analysis showed that the up-regulated genes in the controlled environment population were significantly associated with glucose metabolism, amino acid metabolism, and the nervous system, while those up-regulated in the ex situ population were significantly associated with energy supply and biosynthesis. Further analysis showed that metabolic and hearing-related genes were significantly affected by changes in the environment, and key metabolic genes such as HK, PFK, IDH, and GLS and key hearing-related genes such as OTOA, OTOF, SLC38A1, and GABBR2 were identified. These results suggest that the controlled environment population may have enhanced glucose metabolic ability via activation of glycolysis/gluconeogenesis, the TCA cycle, and inositol phosphate metabolism, while the ex situ population may meet higher energy requirements via enhancement of the amino acid metabolism of the liver and muscle and oxidative phosphorylation. Additionally, the acoustic behavior and auditory-related genes of Yangtze finless porpoise may show responsive changes and differential expression under different environment conditions, and thus the auditory sensitivity may also show corresponding adaptive characteristics. This study provides a new perspective for further exploration of the responsive changes of the two populations to various environments and provides a theoretical reference for further improvements in conservation practices for the Yangtze finless porpoise.

Gapless genome assembly of East Asian finless porpoise

In recent years, conservation efforts have increased for rare and endangered aquatic wildlife, especially cetaceans. However, the East Asian finless porpoise (Neophocaena asiaeorientalis sunameri), which has a wide distribution in China, has received far less attention and protection. As an endangered small cetacean, the lack of a chromosomal-level reference for the East Asian finless porpoise limits our understanding of its population genetics and conservation biology. To address this issue, we combined PacBio HiFi long reads and Hi-C sequencing data to generate a gapless genome of the East Asian finless porpoise that is approximately 2.5 Gb in size over its 21 autosomes and two sex chromosomes (X and Y). A total of 22,814 protein-coding genes were predicted where ~97.31% were functionally annotated. This high-quality genome assembly of East Asian finless porpoise will not only provide new resources for the comparative genomics of cetaceans and conservation biology of threatened species, but also lay a foundation for more speciation, ecology, and evolutionary studies. Measurement(s) Neophocaena asiaeorientalis sunameri • Gapless genome assembly • sequence annotation Technology Type(s) MGISEQ. 2000 • PacBio HiFi Sequencing • Hi-C Sample Characteristic - Organism Neophocaena asiaeorientalis sunameri Sample Characteristic - Environment seawater Sample Characteristic - Location Yellow Sea near Lianyungang City, Jiangsu Province, China.

Underwater Noise Level Recordings from a Water Intake Pontoon and Possible Impacts on Yangtze Finless Porpoises in a Natural Reserve

Underwater noise pollution caused by human activities may affect freshwater cetaceans to different degrees. To analyze the impacts of water intake pontoons on Yangtze finless porpoises (Neophocaena asiaeorientalis), this study collected underwater noise data from such a pontoon in a nature reserve, plotted the power spectral density of acoustic signals, and calculated the root mean square sound pressure levels and the magnitude of sound source levels. The 1/3-octave sound pressure level root mean square values at the transient holding pens were <18.0 kHz, 39.5−60.0 kHz, which were slightly higher than the Yangtze finless porpoise hearing threshold curve values and therefore could be perceived. However, the results indicated that the porpoises would not develop a temporary hearing threshold shift. Meanwhile, pontoon noise did not interfere with the porpoises’ high-frequency acoustic signal nor did it affect their echolocation; it significantly interfered with their low-frequency acoustic signal, however, and the mother−child communication of the finless porpoises was affected, but this effect was quickly compensated due to the limited space range of the holding pens. Through this study of Yangtze finless porpoises, this paper provides a reference for assessing whether human facilities have impacts on freshwater cetaceans.