Full-length transcriptome sequencing from multiple tissues of duck, Anas platyrhynchos

Yin, Zhong-Tao; Zhang, Fan; Smith, Jacqueline; Kuo, Richard; Hou, Zhuocheng

doi:10.1038/s41597-019-0293-1

Cited by 23 publications

(34 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Due to the lack of detailed full-length cDNA data and high-quality genome annotation, there are few studies about AS in ducks or other birds [ 31 , 32 ]. Yin et al (2019) found that a total of 199,993 full-length transcripts were obtained from 8 duck tissues by using transcriptome sequencing, and 35,031 AS events were accurately predicted from 3346 genes, which is very useful for the functional research of other birds [ 33 ]. In our study, an average of 37,267 AS events were counted from each sample, and the number of AS in each sample were mainly concentrated in TSS and TTS, which indicated that the AS of duck skeletal muscle growth and development mainly existed in the first exon and the last exon.…”

Section: Discussionmentioning

confidence: 99%

Comparative Transcriptome Profiling of Skeletal Muscle from Black Muscovy Duck at Different Growth Stages Using RNA-seq

Cao

et al. 2020

Genes

View full text Add to dashboard Cite

In China, the production for duck meat is second only to that of chicken, and the demand for duck meat is also increasing. However, there is still unclear on the internal mechanism of regulating skeletal muscle growth and development in duck. This study aimed to identity candidate genes related to growth of duck skeletal muscle and explore the potential regulatory mechanism. RNA-seq technology was used to compare the transcriptome of skeletal muscles in black Muscovy ducks at different developmental stages (day 17, 21, 27, 31, and 34 of embryos and postnatal 6-month-olds). The SNPs and InDels of black Muscovy ducks at different growth stages were mainly in “INTRON”, “SYNONYMOUS_CODING”, “UTR_3_PRIME”, and “DOWNSTREAM”. The average number of AS in each sample was 37,267, mainly concentrated in TSS and TTS. Besides, a total of 19 to 5377 DEGs were detected in each pairwise comparison. Functional analysis showed that the DEGs were mainly involved in the processes of cell growth, muscle development, and cellular activities (junction, migration, assembly, differentiation, and proliferation). Many of DEGs were well known to be related to growth of skeletal muscle in black Muscovy duck, such as MyoG, FBXO1, MEF2A, and FoxN2. KEGG pathway analysis identified that the DEGs were significantly enriched in the pathways related to the focal adhesion, MAPK signaling pathway and regulation of the actin cytoskeleton. Some DEGs assigned to these pathways were potential candidate genes inducing the difference in muscle growth among the developmental stages, such as FAF1, RGS8, GRB10, SMYD3, and TNNI2. Our study identified several genes and pathways that may participate in the regulation of skeletal muscle growth in black Muscovy duck. These results should serve as an important resource revealing the molecular basis of muscle growth and development in duck.

show abstract

Section: Discussionmentioning

confidence: 99%

Comparative Transcriptome Profiling of Skeletal Muscle from Black Muscovy Duck at Different Growth Stages Using RNA-seq

Cao

et al. 2020

Genes

View full text Add to dashboard Cite

show abstract

“…The combined use of these platforms and library preparation chemistries can generate high-quality and throughput data on full-length transcripts. LRS has been applied for the assembly of transcriptomic maps in several organisms (Sharon et al, 2013 ; Tilgner et al, 2015 ; Sessegolo et al, 2019 ; Yin et al, 2019 ; Zhao et al, 2019 ; Roach et al, 2020 ), including viruses (Tombácz et al, 2016 , 2019 ; Balázs et al, 2017 ; Moldován et al, 2017 ; Prazsák et al, 2018 ; Depledge et al, 2019 ; O'Grady et al, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Short and Long-Read Sequencing Survey of the Dynamic Transcriptomes of African Swine Fever Virus and the Host Cells

et al. 2020

View full text Add to dashboard Cite

“…Amplified cDNA-sequencing -from different time points Samples from each time point (4,8,12, and 20 h p.i.) were sequenced by the ONT MinION device using the cDNA-PCR Barcoding protocol (SQK-PCS109 and SQK-PBK004; Version: PCSB_9086_v109_revK_14Aug2019).…”

Section: Library Preparation For Nanopore Sequencingmentioning

confidence: 99%

Short and Long-read Sequencing Survey of the Dynamic Transcriptomes of African Swine Fever Virus and its Host

Olasz

Tombácz

Torma

et al. 2020

Preprint

View full text Add to dashboard Cite

African swine fever virus (ASFV) is an important animal pathogen causing substantial economic losses in the swine industry globally. At present, little is known about the molecular biology of ASFV, including its transcriptome organization. In this study, we applied cutting-edge sequencing approaches, namely the Illumina short-read sequencing (SRS) and the Oxford Nanopore Technologies long-read sequencing (LRS) techniques, together with several library preparation chemistries to analyze the ASFV dynamic transcriptome. SRS can generate a large amount of high-precision sequencing reads, but it is inefficient for identifying long RNA molecules, transcript isoforms and overlapping transcripts. LRS can overcome these limitations, but this approach also has shortcomings, such as its high error rate and the low coverage. Amplification-based LRS techniques produce relatively high read counts but also high levels of spurious transcripts, whereas the non-amplified cDNA and direct RNA sequencing techniques are more precise but achieve lower throughput. The drawbacks of the various technologies can be circumvented by the combined use of these approaches. Background & SummaryMethodological breakthroughs in sequencing technologies have revolutionized transcriptome profiling in recent years. Currently, the next-generation short-read sequencing (SRS) and third-generation long-read sequencing (LRS) platforms are widely used in genome and transcriptome research. SRS can generate large numbers of sequencing reads with unprecedented speed; however, it cannot sufficiently cover highcomplexity transcriptomes. LRS produces lower data coverage with a higher error rate, but it can overcome many of the drawbacks of SRS, including the inefficiency in distinguishing between transcription isoforms and identifying embedded and long transcripts. The combined use of these platforms and library preparation chemistries can generate high-quality and throughput data on full-length transcripts. LRS has been applied for the assembly of transcriptomic maps in several organisms 1-8 , including viruses 9-17 .African swine fever is a highly lethal animal disease affecting pigs and wild boars. The causative agent of this disease is the large, double-stranded DNA virus, the African swine fever virus (ASFV), the only member of the Asfarviridae family 18 . Because no effective vaccination is currently available against the virus, it is unarguably the largest economic threat to the global pig industry. ASFV is mainly replicates in the cytoplasm, but another form of nuclear replication is also detected in the early phase of the infection 19 . The ASFV genome is 190 kbp long and contains more than 190 open reading frames (ORFs), although the exact numbers of genes and proteins are unknown 20 . Approximately 20 viral genes are believed to participate in transcription and mRNA processing 21 , whereas at least 17 genes play a role in the replication, repair, and modification of DNA 22,23 . Depending on the strain, approximately 30-50 genes are involved in the evasi...

show abstract

Full-length transcriptome sequencing from multiple tissues of duck, Anas platyrhynchos

Cited by 23 publications

References 38 publications

Comparative Transcriptome Profiling of Skeletal Muscle from Black Muscovy Duck at Different Growth Stages Using RNA-seq

Comparative Transcriptome Profiling of Skeletal Muscle from Black Muscovy Duck at Different Growth Stages Using RNA-seq

Short and Long-Read Sequencing Survey of the Dynamic Transcriptomes of African Swine Fever Virus and the Host Cells

Short and Long-read Sequencing Survey of the Dynamic Transcriptomes of African Swine Fever Virus and its Host

Contact Info

Product

Resources

About