Characterization and analysis of the transcriptome in Gymnocypris selincuoensis on the Qinghai-Tibetan Plateau using single-molecule long-read sequencing and RNA-seq

Feng, Xiu; Jia, Yating; Zhu, Ren; Chen, Kang; Chen, Yifeng

doi:10.1093/dnares/dsz014

Cited by 36 publications

(26 citation statements)

References 66 publications

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“…The functional analysis of those selected genes were enriched on the biological pathway of Mismatch repair and Glutathione metabolism, which might reflected the adaptation requirement of high UV radiation for G. namensis in the high altitude habitat. The enrichment on the Mismatch repair was consistent with previous transcriptome analysis for G. selincuoensis, the other high altitude fish species 10 . MutL Homolog 3 (mlh3) (transcript ID of i3_LQ_sample47d422 | c6501/f1p0/3603.p1) and mitochondrial genome maintenance exonuclease 1(mgme1) (transcript ID of i1_LQ_sample47d422 | c51979/f2p0/1450.p1), endonuclease IV (denB) (transcript ID of i2_LQ_sample47d422 | c26034/f1p0/2295.p1) genes were found to be selected for G. namensis.…”

Section: Discussionsupporting

confidence: 90%

“…Recently, Feng et al, used PacBio Iso-Seq and RNA-seq to obtain the high quality full-length transcriptome of G. selincuoensis, the average length and N50 length of full-length transcripts reached 3,509 and 3,870 bp, much longer than that of the de novo assembled transcripts of Illumina RNA-seq for the same fish species (815 and 1,479 bp). Other indicators, such as the percentage of annotated transcripts, are also much higher than that observed in other fishes with RNA-seq 10 . Similarly, compared with the results of transcriptome in the schizothoracinae using the Illumina short-read sequencing, we obtained a longer average transcript length and N50 length (1,819 and 2,044 bp).…”

Section: Discussionmentioning

confidence: 58%

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

Luo

Zhang

et al. 2020

Sci Rep

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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...

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Section: Discussionsupporting

confidence: 90%

Section: Discussionmentioning

confidence: 58%

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

Luo

Zhang

et al. 2020

Sci Rep

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“…Despite the vast amount of sequence data (G. licenti, 34.16 Gb clean data; M. japonicus, 34.55 Gb clean data), fewer unigenes were obtained by PacBio sequencing than by RNA-seq. This phenomenon has also been observed in other FL transcriptome studies 9,48,49 . One of the reasons could be attribute to the strict parameters setting in the process of FL transcript cluster.…”

Section: Discussionsupporting

confidence: 86%

“…In total, 15,803 (87.94%) and 14,846 (88.55%) unigenes were successfully annotated in G. licenti and M. japonicus, respectively ( Table 2 and Additional file 2: table S13 and table S14). By querying the NR database, we analyzed the species containing the identified homologous sequences and found that the largest number of unigenes in G. licenti (7,761,49.82%) and M. japonicus (7,153,48.84%) belonged to Zootermopsis nevadensis (Fig. 5).…”

Section: Alternative Splicing Analysismentioning

confidence: 99%

Characterization and analysis of full-length transcriptomes from two grasshoppers, Gomphocerus licenti and Mongolotettix japonicus

Yuan

Zhang

Zhao

et al. 2020

Sci Rep

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Acrididae are diverse in size, body shape, behavior, ecology and life history; widely distributed; easy to collect; and important to agriculture. they represent promising model candidates for functional genomics, but their extremely large genomes have hindered this research; establishing a reference transcriptome for a species is the primary means of obtaining genetic information. Here, two Acrididae species, Gomphocerus licenti and Mongolotettix japonicus, were selected for full-length (fL) pacBio transcriptome sequencing. for G. licenti and M. japonicus, respectively, 590,112 and 566,165 circular consensus sequences (CCS) were generated, which identified 458,131 and 428,979 full-length nonchimeric (fLnc) reads. After isoform-level clustering, next-generation sequencing (nGS) short sequences were used for error correction, and remove redundant sequences with cD-Hit, 17,970 and 16,766 unigenes were generated for G. licenti and M. japonicus. in addition, we obtained 17,495 and 16,373 coding sequences, 1,082 and 813 transcription factors, 11,840 and 10,814 simple sequence repeats, and 905 and 706 long noncoding RNAs by analyzing the transcriptomes of G. licenti and M. japonicus, respectively, and 15,803 and 14,846 unigenes were annotated in eight functional databases. This is the first study to sequence FL transcriptomes of G. licenti and M. japonicus, providing valuable genetic resources for further functional genomics research. One important goal of functional genomics is to establish relationships between genotypes and phenotypes based on genomic sequence information and various omics techniques 1. The rapid development of high-throughput sequencing technology has greatly facilitated the study of functional genomics, especially the completion of genome sequencing of a large number of species 2-5. However, genome assembly is difficult in species with large genomes, especially those with high heterozygosity and regions with high repeat content 6. Overall, genomic approaches to genotype-phenotype association in species with large genomes still face major challenges. Transcriptomics focuses on the transcribed portion of the genome by sequencing cDNA rather than genomic DNA, thus reducing the size of the sequencing target space, and can be viewed as an alternative to genomic approaches 7. Furthermore, a unique feature of transcriptomics is that it can quantify changes in expression level for each gene among different transcriptome samples. As a low-cost next-generation sequencing (NGS) technology, RNA sequencing (RNA-seq) has become a mainstream tool for studying transcriptomics 8. At present, RNAseq is widely used not only for gene expression profiling, genome annotation and noncoding RNA prediction and quantification but also to gain deep insight into the level of gene expression, the structure of genomic loci, and the sequence variation present at loci (e.g., SNPs) 7. RNA-seq has revolutionized the field of transcriptomics and improved our understanding of genome expression and regulation. Although RNA-seq has bee...

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“…However, a reference transcriptome of L. chinense has not been reported. A reference transcriptome can provide valuable information for researching gene expression and evolution; investigating alternative splicing (AS) events and alternative polyadenylation (APA); and identifying long non-coding RNAs (lncRNAs), fusion transcripts and transcription factors (TFs) [8,9]. The tissue-speci c genes and gene coexpression modules in L. chinense remain unknown.…”

Section: Introductionmentioning

confidence: 99%

Gene co-expression analysis and tissue-specific gene identification in Liriodendron chinense via hybrid sequencing

Tu¹,

Shen²,

Wen³

et al. 2020

Preprint

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Background Liriodendron chinense (Hemsl.) Sarg. is an economically and ecologically important deciduous tree species that has been studied for many years. Although the complete L. chinense genome has been sequenced, the gene co-expression modules and tissue-specific genes of L. chinense remain unknown. Results Here, we used the bracts, petals, sepals, stamens, pistils, leaves, and the shoot apex of L. chinense as materials and analysed their gene co-expression modules and tissue-specific genes via hybrid sequencing. We identified 3,032 DEGs between the floral and vegetative tissues and 2,126 tissue-specific genes. By using WGCNA analysis, we identified 13 gene co-expression modules, and KEGG pathway enrichment analysis revealed that tissue-specific genes and genes from different modules were enriched in different pathways. Genes associated with plant defence were highly expressed in the bracts, genes participating in plant hormone signal transduction were highly expressed in the shoot apex, and genes participating in photosynthesis were highly expressed in the leaves, petals and sepals. Moreover, we identified 10 MIKC-type MADS-box genes that were classified as member of the AP3/PI, SVP, SEP, AG/SHP/STK, AGL12, SOC1 and TM8 subfamily. Phylogenetic analysis showed that the expression profiles of these ten genes were consistent with those reported in Arabidopsis and Populus , indicating that these genes are highly conserved evolutionarily and related to floral and vegetative tissue development. The small number of MIKC-type MADS-box genes in L. chinense was probably owing to its incomplete genome annotation. Conclusions In this work, we provided a reference transcriptome for L. chinense research by using hybrid sequencing. We identified 2,126 tissue-specific genes and 3,032 DEGs that contributed greatly to the functional differences between vegetative organs and floral organs. By using WGCNA analysis, 13 gene co-expression modules and 52 hub genes from six co-expression modules of interest were identified. Moreover, we identified 10 MIKC-type MADS-box genes that might be related to the development and growth regulation of floral and vegetative organs. These findings will improve our understanding of gene co-expression, tissue specific genes and flower development model of L. chinense .

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Characterization and analysis of the transcriptome in Gymnocypris selincuoensis on the Qinghai-Tibetan Plateau using single-molecule long-read sequencing and RNA-seq

Cited by 36 publications

References 66 publications

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

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

Characterization and analysis of full-length transcriptomes from two grasshoppers, Gomphocerus licenti and Mongolotettix japonicus

Gene co-expression analysis and tissue-specific gene identification in Liriodendron chinense via hybrid sequencing

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