Small non-coding RNA transcriptome of four high-altitude vertebrates and their low-altitude relatives

Long, Keren; Feng, Siyuan; Ma, Jideng; Zhang, Jinwei; Jin, Long; Tang, Qianzi; Wang, Xun; Mai, Miaomiao; Xiao, Weihang; Liu, Lingyan; Li, Xuewei; Li, Mingzhou

doi:10.1038/s41597-019-0204-5

Cited by 10 publications

(6 citation statements)

References 24 publications

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“…Therefore, it is of great significance to understand the time spectrum of immune system development in the spleens of domestic pigs. However, only a few reports on the RNA expression of pig spleens have been published [1][2][3][4][5][6].…”

Section: Introductionmentioning

confidence: 99%

Analysis of mRNA and Long Non-Coding RNA Expression Profiles in Developing Yorkshire Pig Spleens

Han

Sun

et al. 2021

Animals

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Epidemic diseases cause great economic loss in pig farms each year; some of these diseases are characterized mainly in the spleen, but mRNA and lncRNA (long non-coding RNA) expression networks in developing Yorkshire pig spleens remain obscure. Here, we profiled the systematic characters of mRNA and lncRNA repertoires in three groups of spleens from nine Yorkshire pigs, each three aged at seven days, 90 days, and 180 days. By using a precise mRNA and lncRNA identification pipeline, we identified 19,647 genes and 219 known and 3219 putative lncRNA transcripts; 1729 genes and 64 lncRNAs therein were found to express differentially. The gene expression characteristics of genes and lncRNAs were found to be basically fixed before 90 days after birth. Three large gene expression modules were detected. The enrichment analyses of differentially expressed genes and the potential target genes of differentially expressed lncRNAs both displayed the crucial roles of up-regulation in immune activation and hematopoiesis, and down-regulation in cell replication and division in 90 days and 180 days compared to seven days. ENSSSCT00000001325 was the only lncRNA transcript that existed in the three groups. CDK1, PCNA, and PLK were detected to be node genes that varied with age. This study contributes to a further understanding of mRNA and lncRNA expression in different developmental pig spleens.

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Section: Introductionmentioning

confidence: 99%

Analysis of mRNA and Long Non-Coding RNA Expression Profiles in Developing Yorkshire Pig Spleens

Han

Sun

et al. 2021

Animals

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“…The number of 306 Rfam small RNA families predicted (with 246 annotated) for the tufted duck in this study is comparable to 352 families predicted in chicken (Gallus gallus, version 5) in Rfam 14.4 [54]. The peaks of transcript length at 20 bp and 50 bp are in the area of microRNA (miRNA), which are usually 18 - 23 nt [55–57], and pre-miRNA which are in the range of 55 - 70 nt. The substantial variance across tissues in our data (many more genes, transcripts and exons in spleen and testis than in the other tissues) might be explained by Illumina sequencing bias introduced at the adapter-ligation step of cDNA library constructions [58, 59].…”

Section: Discussionmentioning

confidence: 66%

A high-quality Genome and Comparison of Short versus Long Read Transcriptome of the Palaearctic duckAythya fuligula(Tufted Duck)

Mueller

Ellström

Howe

et al. 2021

Preprint

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Background: The tufted duck is a non-model organism that suffers high mortality in highly pathogenic avian influenza outbreaks. It belongs to the same bird family (Anatidae) as the mallard, one of the best-studied natural hosts of low-pathogenic avian influenza viruses. Studies in non-model bird species are crucial to disentangle the role of the host response in avian influenza virus infection in the natural reservoir. Such endeavour requires a high-quality genome assembly and transcriptome. Results: This study presents the first high-quality, chromosome-level reference genome assembly of the tufted duck using the Vertebrate Genomes Project pipeline. We sequenced RNA (cDNA) from brain, ileum, lung, ovary, spleen and testis using Illumina short-read and PacBio long-read sequencing platforms, which was used for annotation. We found 34 autosomes plus Z and W sex chromosomes in the curated genome assembly, with 99.6% of the sequence assigned to chromosomes. Functional annotation revealed 14,099 protein-coding genes that generate 111,934 transcripts, which implies an average of 7.9 isoforms per gene. We also identified 246 small RNA families. Conclusions: This annotated genome contributes to continuing research into the host response in avian influenza virus infections in a natural reservoir. Our findings from a comparison between short-read and long-read reference transcriptomics contribute to a deeper understanding of these competing options. In this study, both technologies complemented each other. We expect this annotation to be a foundation for further comparative and evolutionary genomic studies, including many waterfowl relatives with differing susceptibilities to the avian influenza virus.

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“…The protein-encoding genes and miRNA expression profile data of six tissues (muscle, liver, heart, spleen, kidneys, and lungs) from three Tibetan pigs and three Rongchang pigs were obtained from the Gene Expression Omnibus (GEO) database at the National Center for Biotechnology Information (NCBI) under accession numbers GSE93855 (provided by Tang et al, 2017) and GSE124418 (uploaded by Long et al, 2019), respectively. For details about the experimental animals, please refer to the Supplementary Material.…”

Section: Gene Expression Data Collectionmentioning

confidence: 99%

KLF4, a Key Regulator of a Transitive Triplet, Acts on the TGF-β Signaling Pathway and Contributes to High-Altitude Adaptation of Tibetan Pigs

et al. 2021

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Tibetan pigs are native mammalian species on the Tibetan Plateau that have evolved distinct physiological traits that allow them to tolerate high-altitude hypoxic environments. However, the genetic mechanism underlying this adaptation remains elusive. Here, based on multitissue transcriptional data from high-altitude Tibetan pigs and low-altitude Rongchang pigs, we performed a weighted correlation network analysis (WGCNA) and identified key modules related to these tissues. Complex network analysis and bioinformatics analysis were integrated to identify key genes and three-node network motifs. We found that among the six tissues (muscle, liver, heart, spleen, kidneys, and lungs), lung tissue may be the key organs for Tibetan pigs to adapt to hypoxic environment. In the lung tissue of Tibetan pigs, we identified KLF4, BCL6B, EGR1, EPAS1, SMAD6, SMAD7, KDR, ATOH8, and CCN1 genes as potential regulators of hypoxia adaption. We found that KLF4 and EGR1 genes might simultaneously regulate the BCL6B gene, forming a KLF4–EGR1–BCL6B complex. This complex, dominated by KLF4, may enhance the hypoxia tolerance of Tibetan pigs by mediating the TGF-β signaling pathway. The complex may also affect the PI3K-Akt signaling pathway, which plays an important role in angiogenesis caused by hypoxia. Therefore, we postulate that the KLF4–EGR1–BCL6B complex may be beneficial for Tibetan pigs to survive better in the hypoxia environments. Although further molecular experiments and independent large-scale studies are needed to verify our findings, these findings may provide new details of the regulatory architecture of hypoxia-adaptive genes and are valuable for understanding the genetic mechanism of hypoxic adaptation in mammals.

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Small non-coding RNA transcriptome of four high-altitude vertebrates and their low-altitude relatives

Cited by 10 publications

References 24 publications

Analysis of mRNA and Long Non-Coding RNA Expression Profiles in Developing Yorkshire Pig Spleens

Analysis of mRNA and Long Non-Coding RNA Expression Profiles in Developing Yorkshire Pig Spleens

A high-quality Genome and Comparison of Short versus Long Read Transcriptome of the Palaearctic duckAythya fuligula(Tufted Duck)

KLF4, a Key Regulator of a Transitive Triplet, Acts on the TGF-β Signaling Pathway and Contributes to High-Altitude Adaptation of Tibetan Pigs

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