Full-length transcript sequencing accelerates the transcriptome research of Gymnocypris namensis, an iconic fish of the Tibetan Plateau

Abstract

Gymnocypris namensis, the only commercial fish in Namtso Lake of Tibet in China, is rated as nearly threatened species in the Red List of China's Vertebrates. As one of the highest-altitude schizothorax fish in China, G. namensis has strong adaptability to the plateau harsh environment. Although being an indigenous economic fish with high value in research, the biological characterization, genetic diversity, and plateau adaptability of G. namensis are still unclear. Here, we used Pacific Biosciences single molecular real time long read sequencing technology to generate full-length transcripts of G. namensis. Sequences clustering analysis and error correction with Illumina-produced short reads to obtain 319,044 polished isoforms. After removing redundant reads, 125,396 non-redundant isoforms were obtained. Among all transcripts, 103,286 were annotated to public databases. Natural selection has acted on 42 genes for G. namensis, which were enriched on the functions of mismatch repair and Glutathione metabolism. Total 89,736 open reading frames, 95,947 microsatellites, and 21,360 long non-coding RNAs were identified across all transcripts. This is the first study of transcriptome in G. namensis by using PacBio Iso-seq. The acquisition of full-length transcript isoforms might accelerate the transcriptome research of G. namensis and provide basis for further research. The Tibetan Plateau, a harsh environment with an average altitude of 4,500 m, is home to the highest and largest high-altitude lakes in the world 1,2. The area of lakes on the Tibetan Plateau are more than 50,900 km 2 , and 1,091 lakes are larger than 1.0 km 2,3. With an area of 1,920 km 2 and an altitude of 4,718 m, Namtso Lake in the North Tibet is the highest great lake in the world and is the second biggest salt water lake in China 4,5. As a highly natural, rare, fragile and representative lake, Namtso Lake imposes many inhospitable living conditions on most of organisms, such as the high pH and alkalinity, severe cold (with an annual average temperature of 0°C, five-month ice-covered period), the low primary productivity and oligotrophic conditions 3-7. Because of the lower temperatures and oligotrophic conditions of Namtso Lake, only two endemic fish species (Gymnocypris namensis and Triplophysa stewarti) have been found in the lake 6. G. namensis, the only economic fish in Namtso Lake, is known as one of the highest-altitude schizothorax fish in China and it has strong ability to adapt to the plateau harsh environment 6,8. However, systematic biological studies on G. namensis are chronically lacked due to extremely harsh environments on the plateau 8,9. In previous transcriptome studies in other fish of geneus Gymnocypris, such as Gymnocypris selincuoensis 10 , Gymnocypris przewalskii 11 , Gymnocypris eckloni 12 , some progress has been made. In transcriptome studies of G. selincuoensis, a full-length reference transcriptome has been generated by using PacBio Iso-Seq and Illumina RNA-seq technologies. But the most of other transcriptome studies us...

Genetic Variation in Schizothorax kozlovi Nikolsky in the Upper Reaches of the Chinese Yangtze River Based on Genotyping for Simplified Genome Sequencing

“…Several types of functional selection genes are involved in the regulation of temperature changes by processes such as signal transduction, energy metabolism, and membrane [ 44 ]. Specifically, transcriptome research on Gymnocypris namensis [ 52 ] and Gymnocypris selincuoensis [ 53 ] demonstrated similar results. In our study, the common molecular pathways of selected SNPs among the YL vs. WJ, JS vs. WJ, and JS vs. YL groups of S. kozlovi populations were enriched in the cellular process (3 signaling pathways), environmental adaptation (circadian rhythm), signal transduction (4 signaling pathways), and related metabolism GO terms (such as mitochondrial translation and mitochondrial transport).…”

Genomic insights into the adaptive and convergent evolution of Leuciscus waleckii inhabiting extremely alkaline environments

“…Based on the smaller population (in particular, a lower recombination rate or lower level of nucleotide diversity in the genome) and adaptation to an extreme alkali environment, we proposed two possible hypotheses to explain the more conserved Rhcga protein sequences in the alkaline papulation: 1. genetic drift and 2. selective sweep. Fortunately, in addition to Amor Ide living in such an alkaline water area, previous studies have determined that other teleost species have evolved some characteristics to survive in the same lake ( Triplophysa dalaica and Carassius auratus ) or other similar conditions ( Gymnocypris przewalskii in Qinghai Lake) 9,62,63 . With sufficient genetic information on these different species living under similar conditions, we checked all the rhcga alignments based on sequence similarity and discovered high convergence among four alkaline survivors at two of the seven loci that differentiated freshwater and alkali-water L. waleckii populations.…”

SMRT sequencing of the full-length transcriptome of Gekko gecko

“…Moreover, SMRT sequencing provides accurate fulllength transcripts, and average sequence read that up to 50 kb have been reported [13,14]. Therefore, SMRT sequencing represents an effective tool that has been widely and successfully used to annotate and analyze full-length transcripts among mammals, marine animals, aquatic animals and insects [15], such as Tachypleus tridentatus [16], Pinctada fucata martensii [12], Sogatella furcifera [17], and Odontotermes formosanu [18][19][20]. However, no studies have investigated on G. gecko.…”