Transcriptome profiling of the Macrobrachium rosenbergii lymphoid organ under the white spot syndrome virus challenge

Cao, Jun; Wu, Lei; Jin, Min; Li, Tingting; Hui, Kai-Min; Ren, Qian

doi:10.1016/j.fsi.2017.05.059

Cited by 36 publications

(26 citation statements)

References 107 publications

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“…Hui et al used transcriptome analysis to reveal a large number of immune-related genes in the intestine of M. rosenbergii infected with WSSV ( 40 ). By using transcriptome sequencing, Cao et al also obtained an abundant number of immune-related genes, such as toll-like receptors, C-type lectins, and scavenger receptors, during WSSV infection of M. rosenbergii ( 41 ). In the present study, transcriptome analysis was conducted to identify genes and pathways in L. vannamei which may play a role during the infection of DIV1.…”

Section: Discussionmentioning

confidence: 99%

Comparative Transcriptome Analysis of Litopenaeus vannamei Reveals That Triosephosphate Isomerase-Like Genes Play an Important Role During Decapod Iridescent Virus 1 Infection

Liao

Wang

et al. 2020

Front. Immunol.

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Decapod iridescent virus 1 (DIV1) results in severe economic losses in shrimp aquaculture. However, little is known about the physiological effect of DIV1 infection on the host. In this study, we found that the lethal dose 50 of DIV1-infected Litopenaeus vannamei after 48, 72, 96, and 156 h were 4.86 × 10 6 , 5.07 × 10 5 , 2.13 × 10 5 , and 2.38 × 10 4 copies/μg DNA, respectively. In order to investigate the mechanisms of DIV1 infection, a comparative transcriptome analysis of hemocytes from L. vannamei , infected or not with DIV1, was conducted. The BUSCO analysis showed that the transcriptome was with high completeness (complete single-copy BUSCOs: 57.3%, complete duplicated BUSCOs: 41.1%, fragmentation: 0.8%, missing: 0.8%). A total of 168,854 unigenes were assembled, with an average length of 601 bp. Based on homology searches, Kyoto Encyclopedia of Genes and Genomes (KEGG), gene ontology (GO), and cluster of orthologous groups of proteins (KOG) analysis, 62,270 (36.88%) unigenes were annotated. Among them, 1,112 differentially expressed genes (DEGs) were identified, of which 889 genes were up-regulated and 223 genes were down-regulated after DIV1 infection. These genes were mainly annotated to the major metabolic processes such as fructose and mannose metabolism, carbon metabolism, and inositol phosphate metabolism. Among these metabolic pathways, the triosephosphate isomerase ( TPI ) family was the most eye-catching DEG as it participates in several metabolic processes. Three types of TPI, LvTPI-like, LvTPI-Blike , and LvTPI-Blike1 , were obtained for gene silencing by RNA interference. The results showed that LvTPI-like and LvTPI-Blike1 silencing caused a high mortality rate among L. vannamei . However, LvTPI-like and LvTPI-Blike silencing reduced DIV1 replication in DIV1-infected L. vannamei . All the results indicated that TPI-like genes play an important role during DIV1 infection, which provides valuable insight into the infection mechanism of DIV1 in shrimp and may aid in preventing viral diseases in shrimp culture.

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Section: Discussionmentioning

confidence: 99%

Comparative Transcriptome Analysis of Litopenaeus vannamei Reveals That Triosephosphate Isomerase-Like Genes Play an Important Role During Decapod Iridescent Virus 1 Infection

Liao

Wang

et al. 2020

Front. Immunol.

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“…Mating of sex-reversed females (neo-males) with normal females (ZW) could increase a higher ratio of females, while mating of sex-reversed males (neo-females) with normal males could produce all-male (ZZ × ZZ) progeny [1,6,7]. Recently, along with the emergence of high-throughput sequencing, RNA-seq as a most powerful tool is available for illustrating the mechanisms of immune response [35], determining the expression pattern of reproduction, growth, and pheromone communication in hepatopancreas, gill, muscle, and antennal gland [36][37][38]. In the present study, we profiled to detect the transcriptomes of gonads in females, super females, and the males using RNA-seq, with the aim of interpreting the molecular mechanism involved in the sex determination, and identifying sex-related candidate genes.…”

Section: Discussionmentioning

confidence: 99%

Comparative Transcriptome Analysis of Gonads for the Identification of Sex-Related Genes in Giant Freshwater Prawns (Macrobrachium Rosenbergii) Using RNA Sequencing

Jiang

Yuan

Qingqing

et al. 2019

Genes

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The giant freshwater prawn (Macrobrachium rosenbergii) exhibits sex dimorphism between the male and female individuals. To date, the molecular mechanism governing gonadal development was unclear, and limited data were available on the gonad transcriptome of M. rosenbergii. Here, we conducted comprehensive gonadal transcriptomic analysis of female (ZW), super female (WW), and male (ZZ) M. rosenbergii for gene discovery. A total of 70.33 gigabases (Gb) of sequences were generated. There were 115,338 unigenes assembled with a mean size of 1196 base pair (bp) and N50 of 2195 bp. Alignment against the National Center for Biotechnology Information (NCBI) non-redundant nucleotide/protein sequence database (NR and NT), the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, SwissProt database, Protein family (Pfam), Gene ontology (GO), and the eukaryotic orthologous group (KOG) database, 36,282 unigenes were annotated at least in one database. Comparative transcriptome analysis observed that 10,641, 16,903, and 3393 genes were significantly differentially expressed in ZW vs. ZZ, WW vs. ZZ, and WW vs. ZW samples, respectively. Enrichment analysis of differentially expressed genes (DEGs) resulted in 268, 153, and 42 significantly enriched GO terms, respectively, and a total of 56 significantly enriched KEGG pathways. Additionally, 23 putative sex-related genes, including Gtsf1, IR, HSP21, MRPINK, Mrr, and other potentially promising candidate genes were identified. Moreover, 56,241 simple sequence repeats (SSRs) were identified. Our findings provide a valuable archive for further functional analyses of sex-related genes and future discoveries of underlying molecular mechanisms of gonadal development and sex determination. delicious flesh and high value nutrition. Like other crustaceans, M. rosenbergii displays sexual dimorphic growth pattern: The male individuals grow much larger and faster than the females [1,2]. Thus, based on the economic impact, developing the monosex population culture as the efficient approach to boost production has received great attention from researchers in M. rosenbergii. Nevertheless, the premise of monosex culture is to understand the molecular mechanism of sex determination, as well as to unravel sex-related genes.Studies on sex determination have proved that many macruran species exhibit the ZW/ZZ sex determination system [3][4][5]. In M. rosenbergii, sex reversal experiments proposed that the female prawns bear the ZW sex chromosomes, and the male individuals bear the ZZ chromosomes [1,6,7]. Subsequently, isolation of sex-specific markers further deepened the insight of the ZW/ZZ sex determination mode [8,9]. Recently, Ma et al. have confirmed that M. rosenbergii has the ZW/ZZ sex determination system based on the bacterial artificial chromosome (BAC) library, and nine genes were unraveled to be the key sex-linked genes by PacBio sequencing. Amongst, three genes, including zinc knuckle domain (ZKD), reverse transcriptase, and ANCDUO, protein homologs were known genes without characteri...

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“…The circRNAs were identified according to the following computational pipeline: First, the raw reads were mapped to a human reference genome hg38 (GRCh38.p7) using TopHat (v2.1.0) to exclude the linear transcripts (ftp://ftp.ensembl.org/pub/release-85/fasta/homo_sapiens/) [30]. Second, the unmapped reads were aligned to the human reference genome hg38 (GRCh38.p7) to identify the fusion transcripts using TopHat-Fusion (v2.1.0).…”

Section: In Silico Identification and Differential Expression Analysimentioning

confidence: 99%

Deep RNA Sequencing Reveals a Repertoire of Human Fibroblast Circular RNAs Associated with Cellular Responses to Herpes Simplex Virus 1 Infection

Shi¹,

Hu²,

Mo³

et al. 2018

Cell Physiol Biochem

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Background/Aims: Circular RNAs (circRNAs), a new class of regulators of gene expression, are involved in diverse physiological and pathogenic processes. However, their role in cellular responses to virus infection is yet unclear. Methods: A human lung fibroblast cell line was infected or mock infected by herpes simplex virus 1 (HSV-1). Deep RNA sequencing was used to profile the global changes in circRNAs, genes, and miRNAs following HSV-1 infection. Altered circRNAs, genes, and miRNAs were validated using quantitative reverse transcription polymerase chain reaction (RT-qPCR). An integration analysis of circRNAs, genes, and miRNAs was applied to investigate the putative function of the dysregulated circRNAs. Results: A total of 536 circRNAs, 3,885 genes, and 207 miRNAs were significantly dysregulated after HSV-1 infection. An integration analysis of circRNAs, genes, and miRNAs revealed the alleged involvement of dysregulated circRNAs in cellular responses to HSV-1 infection via the circRNA-miRNA-gene regulatory axis. These genes regulated by circRNAs were enriched to NOD-like receptor/JAK-STAT signaling pathway, and pathways of apoptosis, cell cycle progression, and cell death, all of which may be implicated in the viral pathogenesis and cellular immunity. Conclusions: These data present a comprehensive view for circRNAs induced by HSV-1 and their interplay with miRNAs and genes during HSV-1 infection, thus offering new insights into the mechanisms of interactions between HSV-1 and the host.

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Transcriptome profiling of the Macrobrachium rosenbergii lymphoid organ under the white spot syndrome virus challenge

Cited by 36 publications

References 107 publications

Comparative Transcriptome Analysis of Litopenaeus vannamei Reveals That Triosephosphate Isomerase-Like Genes Play an Important Role During Decapod Iridescent Virus 1 Infection

Comparative Transcriptome Analysis of Litopenaeus vannamei Reveals That Triosephosphate Isomerase-Like Genes Play an Important Role During Decapod Iridescent Virus 1 Infection

Comparative Transcriptome Analysis of Gonads for the Identification of Sex-Related Genes in Giant Freshwater Prawns (Macrobrachium Rosenbergii) Using RNA Sequencing

Deep RNA Sequencing Reveals a Repertoire of Human Fibroblast Circular RNAs Associated with Cellular Responses to Herpes Simplex Virus 1 Infection

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