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

Abstract The lakes on the Qinghai-Tibet Plateau (QTP) are the largest and highest lake group in the world. Gymnocypris selincuoensis is the only cyprinid fish living in lake Selincuo, the largest lake on QTP. However, its genetic resource is still blank, limiting studies on molecular and genetic analysis. In this study, the transcriptome of G. selincuoensis was first generated by using PacBio Iso-Seq and Illumina RNA-seq. A full-length (FL) transcriptome with 75,435 transcripts was obtained by Iso-Seq with N50 length of 3,870 bp. Among all transcripts, 75,016 were annotated to public databases, 64,710 contain complete open reading frames and 2,811 were long non-coding RNAs. Based on all- vs.-all BLAST, 2,069 alternative splicing events were detected, and 80% of them were validated by reverse transcription polymerase chain reaction (RT-PCR). Tissue gene expression atlas showed that the number of detected expressed transcripts ranged from 37,397 in brain to 19,914 in muscle, with 10,488 transcripts detected in all seven tissues. Comparative genomic analysis with other cyprinid fishes identified 77 orthologous genes with potential positive selection (Ka/Ks > 0.3). A total of 56,696 perfect simple sequence repeats were identified from FL transcripts. Our results provide valuable genetic resources for further studies on adaptive evolution, gene expression and population genetics in G. selincuoensis and other congeneric fishes.

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The RNA-Seq-based high resolution gene expression atlas of chickpea (Cicer arietinum L.) reveals dynamic spatio-temporal changes associated with growth and development

Plant Cell & Environment ◽

10.1111/pce.13210 ◽

2018 ◽

Cited By ~ 15

Author(s):

Himabindu Kudapa ◽

Vanika Garg ◽

Annapurna Chitikineni ◽

Rajeev K. Varshney

Keyword(s):

Gene Expression ◽

High Resolution ◽

Cicer Arietinum ◽

Growth And Development ◽

Temporal Changes ◽

Rna Seq ◽

Cicer Arietinum L ◽

Gene Expression Atlas ◽

Expression Atlas ◽

Spatio Temporal

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Gene expression atlas of fruit ripening of octoploid strawberry (Fragaria×ananassa) and transcriptome assembly from RNA-seq data

New Biotechnology ◽

10.1016/j.nbt.2016.06.1261 ◽

2016 ◽

Vol 33 ◽

pp. S156

Author(s):

José Federico Sánchez Sevilla ◽

José G. Vallarino ◽

Sonia Osorio ◽

Aureliano Bombarely ◽

Katharina Merchante ◽

...

Keyword(s):

Gene Expression ◽

Fruit Ripening ◽

Transcriptome Assembly ◽

Fragaria Ananassa ◽

Rna Seq ◽

Gene Expression Atlas ◽

Expression Atlas

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Full-lengthde novoassembly of RNA-seq data in pea (Pisum sativumL.) provides a gene expression atlas and gives insights into root nodulation in this species

The Plant Journal ◽

10.1111/tpj.12967 ◽

2015 ◽

Vol 84 (1) ◽

pp. 1-19 ◽

Cited By ~ 82

Author(s):

Susete Alves-Carvalho ◽

Grégoire Aubert ◽

Sébastien Carrère ◽

Corinne Cruaud ◽

Anne-Lise Brochot ◽

...

Keyword(s):

Gene Expression ◽

Rna Seq ◽

Root Nodulation ◽

Gene Expression Atlas ◽

Expression Atlas

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The Vigna unguiculata Gene Expression Atlas (Vu GEA ) from de novo assembly and quantification of RNA ‐seq data provides insights into seed maturation mechanisms

The Plant Journal ◽

10.1111/tpj.13279 ◽

2016 ◽

Vol 88 (2) ◽

pp. 318-327 ◽

Cited By ~ 21

Author(s):

Shaolun Yao ◽

Chuan Jiang ◽

Ziyue Huang ◽

Ivone Torres‐Jerez ◽

Junil Chang ◽

...

Keyword(s):

Gene Expression ◽

Vigna Unguiculata ◽

De Novo Assembly ◽

De Novo ◽

Seed Maturation ◽

Rna Seq ◽

Gene Expression Atlas ◽

Expression Atlas

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An RNA-Seq based gene expression atlas of the common bean

BMC Genomics ◽

10.1186/1471-2164-15-866 ◽

2014 ◽

Vol 15 (1) ◽

pp. 866 ◽

Cited By ~ 73

Author(s):

Jamie A O’Rourke ◽

Luis P Iniguez ◽

Fengli Fu ◽

Bruna Bucciarelli ◽

Susan S Miller ◽

...

Keyword(s):

Gene Expression ◽

Common Bean ◽

Rna Seq ◽

Gene Expression Atlas ◽

Expression Atlas ◽

The Common

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Gene expression atlas of fruit ripening and transcriptome assembly from RNA-seq data in octoploid strawberry (Fragaria × ananassa)

Scientific Reports ◽

10.1038/s41598-017-14239-6 ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 36

Author(s):

José F. Sánchez-Sevilla ◽

José G. Vallarino ◽

Sonia Osorio ◽

Aureliano Bombarely ◽

David Posé ◽

...

Keyword(s):

Gene Expression ◽

Fruit Ripening ◽

Transcriptome Assembly ◽

Fragaria Ananassa ◽

Rna Seq ◽

Gene Expression Atlas ◽

Expression Atlas

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Melonet-DB, a Grand RNA-Seq Gene Expression Atlas in Melon (Cucumis melo L.)

Plant and Cell Physiology ◽

10.1093/pcp/pcx193 ◽

2017 ◽

Vol 59 (1) ◽

pp. e4-e4 ◽

Cited By ~ 16

Author(s):

Ryoichi Yano ◽

Satoko Nonaka ◽

Hiroshi Ezura

Keyword(s):

Gene Expression ◽

Cucumis Melo ◽

Rna Seq ◽

Gene Expression Atlas ◽

Expression Atlas ◽

Cucumis Melo L

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Widespread polycistronic transcripts in mushroom-forming fungi revealed by single-molecule long-read mRNA sequencing

10.1101/012542 ◽

2014 ◽

Cited By ~ 1

Author(s):

Sean Gordon ◽

Elizabeth Tseng ◽

Asaf Salamov ◽

Jiwei Zhang ◽

Xiandong Meng ◽

...

Keyword(s):

Single Molecule ◽

Genomic Analysis ◽

Fungal Species ◽

Comparative Genomic ◽

Bioinformatics Pipeline ◽

Polycistronic Transcription ◽

Long Read ◽

Sequencing Strategy ◽

Polycistronic Transcripts ◽

Mrna Isoform

Genes in prokaryotic genomes are often arranged into clusters and co-transcribed into polycistronic RNAs. Isolated examples of polycistronic RNAs were also reported in some eukaryotes but their presence was generally considered rare. Here we developed a long-read sequencing strategy to identify polycistronic transcripts in several mushroom forming fungal species including Plicaturopsis crispa, Phanerochaete chrysosporium, Trametes versicolor and Gloeophyllum trabeum1. We found genome-wide prevalence of polycistronic transcription in these Agaricomycetes, and it involves up to 8% of the transcribed genes. Unlike polycistronic mRNAs in prokaryotes, these co-transcribed genes are also independently transcribed, and upstream transcription may interfere downstream transcription. Further comparative genomic analysis indicates that polycistronic transcription is likely a feature unique to these fungi. In addition, we also systematically demonstrated that short-read assembly is insufficient for mRNA isoform discovery, especially for isoform-rich loci. In summary, our study revealed, for the first time, the genome prevalence of polycistronic transcription in a subset of fungi. Futhermore, our long-read sequencing approach combined with bioinformatics pipeline is a generic powerful tool for precise characterization of complex transcriptomes.

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Elimination of reference mapping bias reveals robust immune related allele-specific expression in crossbred sheep

10.1101/619122 ◽

2019 ◽

Cited By ~ 1

Author(s):

Mazdak Salavati ◽

Stephen J. Bush ◽

Sergio Palma-Vera ◽

Mary E. B. McCulloch ◽

David A. Hume ◽

...

Keyword(s):

Gene Expression ◽

Complex Traits ◽

Allelic Imbalance ◽

Cell Types ◽

Rna Seq ◽

Specific Expression ◽

Allele Specific Expression ◽

Gene Expression Atlas ◽

Expression Atlas ◽

Allele Specific

AbstractPervasive allelic variation at both gene and single nucleotide level (SNV) between individuals is commonly associated with complex traits in humans and animals. Allele-specific expression (ASE) analysis, using RNA-Seq, can provide a detailed annotation of allelic imbalance and infer the existence of cis-acting transcriptional regulation. However, variant detection in RNA-Seq data is compromised by biased mapping of reads to the reference DNA sequence. In this manuscript we describe an unbiased standardised computational pipeline for allele-specific expression analysis using RNA-Seq data, which we have adapted and developed using tools available under open licence. The analysis pipeline we present is designed to minimise reference bias while providing accurate profiling of allele-specific expression across tissues and cell types. Using this methodology, we were able to profile pervasive allelic imbalance across tissues and cell types, at both the gene and SNV level, in Texel x Scottish Blackface sheep, using the sheep gene expression atlas dataset. ASE profiles were pervasive in each sheep and across all tissue types investigated. However, ASE profiles shared across tissues were limited and instead they tended to be highly tissue-specific. These tissue-specific ASE profiles may underlie the expression of economically important traits and could be utilized as weighted SNVs, for example, to improve the accuracy of genomic selection in breeding programmes for sheep. An additional benefit of the pipeline is that it does not require parental genotypes and can therefore be applied to other RNA-Seq datasets for livestock, including those available on the Functional Annotation of Animal Genomes (FAANG) data portal. This study is the first global characterisation of moderate to extreme ASE in tissues and cell types from sheep. We have applied a robust methodology for ASE profiling, to provide both a novel analysis of the multi-dimensional sheep gene expression atlas dataset, and a foundation for identifying the regulatory and expressed elements of the genome that are driving complex traits in livestock.

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