Comparative Analysis of Blood Transcriptome in the Yangtze Finless Porpoise (Neophocaena asiaeorientalis)

Di-An Fang,Pao Xu,Yin-Ping Wang,Kai Liu,Dong-Po Xu

doi:10.3390/fishes7020061

Abstract

The Yangtze finless porpoise (Neophocaena asiaeorientalis) is the sole freshwater subspecies of Neophocaenaphocaenoides, and there is a lack of data on its transcriptome. In this study, we applied RNA-seq technology to assemble, de novo, a transcriptome and analyzed differential expressed genes (DEGs). About 6 Gb of clean data was generated for the Yangtze finless porpoise blood (n = 6) through de novo sequencing. In total, 151,211 unigenes were generated and a total of 119,039 of these unigenes (78.72%) were functionally annotated when searched for within the NCBI Nr, SwissProt, GO, COG, and KEGG databases. Diverse and extensive expressed gene catalogs were sampled for the Yangtze finless porpoise. DESeq2 was used to analyze the differential expression genes (DEGs) obtained from the assembled transcriptome. The results indicated that DEGs have close relationships with the Yangtze finless porpoise’s development, evolution and adaptation. Further, we found that genes involved in cetacean TAG synthesis might directly explain the molecular basis of cetacean blubber thickening. These transcriptome data will assist in understanding molecular mechanisms of Yangtze finless porpoise adaptation.

Highlights

The Yangtze finless porpoise (Neophocaena asiaeorientalis) is the sole freshwater subspecies of Neophocaena phocaenoides, is listed as a critically endangered species in the IUCNRed List of Threatened Species [1] and has been shown to be a unique incipient species [2]
When the assembled transcriptome was combined together for DGEs enrichment pathway analysis using the DEseq2 method, the results showed higher unigene expression involved in environmental information processing
The results showed that acylglycerol-3-phosphate O-acyltransferase 1 (AGPAT1), PLCd1 and PPARa mRNA transcript expression was significantly higher in the older Yangtze finless porpoises than in the younger ones, which is consistent with the results of differential expressed genes (DEGs) expression analysis

Summary

Introduction

The Yangtze finless porpoise (Neophocaena asiaeorientalis) is the sole freshwater subspecies of Neophocaena phocaenoides, is listed as a critically endangered species in the IUCNRed List of Threatened Species [1] and has been shown to be a unique incipient species [2]. The Yangtze finless porpoise (Neophocaena asiaeorientalis) is the sole freshwater subspecies of Neophocaena phocaenoides, is listed as a critically endangered species in the IUCN. Its population size has decreased remarkably because of water development projects, water pollution, overfishing and accidental deaths during the last several decades [3–6]. It was estimated that the remaining population was approximately 1200 in 2006, decreasing at a rate about 5% per year [4]. The disconnection between lakes and the Yangtze River has directly impacted the ecosystem functions related to Yangtze finless porpoise habitats [7]. A plan for Yangtze finless porpoise conservation was approved by the Chinese government and developed by scientists from the Institute of Hydrobiology (CAS) [8,9]. Captive breeding programs have served as a valuable and effective protection method and provide vital help for the conservation of this species [9]

Methods

Results

Conclusion