Analysis of Litopenaeus vannamei Transcriptome Using the Next-Generation DNA Sequencing Technique

Li, Chaozheng; Weng, Shaoping; Chen, Yong-Gui; Yu, Xiao‐Qiang; Lü, Ling; Zhang, Haiqing; He, Jianguo; Xu, Xiaopeng

doi:10.1371/journal.pone.0047442

Cited by 118 publications

(114 citation statements)

References 54 publications

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“…GO is an international, standardized functional gene classification system, which offers a dynamically updated controlled vocabulary and a strictly defined concept to comprehensively describe the properties of genes and their products in any organism (Ye et al, 2006;Li et al, 2012). Based on the sequence homology, 18,153 (43.58%) unigenes were assigned to three functional groups based on their GO terminology: biological processes, molecular functions, and cellular components (Figure 1 and Table S2).…”

Section: Resultsmentioning

confidence: 99%

Transcriptome sequencing and analysis of the coconut leaf beetle, Brontispa longissima

Wang¹,

Liu²,

Li³

et al. 2015

Genet. Mol. Res.

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ABSTRACT. The coconut leaf beetle, Brontispa longissima, is a destructive pest of palm plants. Although its ecological and biological characteristics are well understood, its genetic information remains largely unknown. To advance our understanding of its molecular basis of biology and ecology, we sequenced and analyzed its whole transcriptome by using high-throughput Illumina paired-end sequencing technology. Approximately 8.08 Gb of clean reads were generated in a single run, which were assembled by using Trinity into 41,652 unigenes with an average length of 932 bp. By sequence similarity searches for known proteins, 23,077 (55.4%) unigenes were annotated by BLASTx searches against the NCBI non-redundant protein database. Of the unigenes assembled, 18,153 and 13,733 were assigned to Gene Ontology and Clusters of Orthologous Groups of proteins, respectively. In addition, 10,415 unigenes were mapped onto 247 pathways using the W. Yan et al. 8360©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (3): 8359-8365 (2015) Kyoto Encyclopedia of Genes and Genomes Pathway database. These transcriptomic resources will facilitate gene identification and elucidate the molecular mechanisms of biological and ecological aspects underlying this palm pest, in order to design a new control strategy.

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Section: Resultsmentioning

confidence: 99%

Transcriptome sequencing and analysis of the coconut leaf beetle, Brontispa longissima

Wang¹,

Liu²,

Li³

et al. 2015

Genet. Mol. Res.

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“…However, it seems clear that Antennapedia is present in crustaceans, as this gene was identified in two Branchiopoda (D. Pulex and Artemia franciscana) and in the amphipod Parhyale hawaiensis. In addition, this gene is present in decapoda and was detected in L. vannamei as expressed only during the gastrula stage (215 minutes post spawning) in early embryo development (Li et al, 2012).…”

Section: Proteins In P Leniusculus Hematopoiesis -A Comparison With mentioning

confidence: 99%

Crustacean hematopoiesis

Söderhäll

2016

Developmental & Comparative Immunology

168

138

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Crustacean hemocytes are important mediators of immune reactions, and the regulation of hemocyte homeostasis is of utmost importance for the health of these animals. This review discusses the current knowledge on the lineages, synthesis and differentiation of hemocytes in crustaceans. Hematopoietic tissues, their origins, and the regulation of hematopoiesis during molting, seasonal variation and infection are discussed. Furthermore, studies concerning the molecular regulation of hemocyte formation in crustaceans are also described, and the different lineages and their molecular markers are discussed and compared with several insect species. Signaling pathways and the regulation of hematopoiesis by transcription factors are typically conserved among these arthropods, whereas cytokines and growth factors are more variable and species specific. However, considering the great diversity among the crustaceans, one should be cautious in drawing general conclusions from studies of only a few species.2

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“…uni-bielefeld.de/rnahybrid/submission.html) (37) based on the transcriptome of L. vannamei (38). PremiR-1959 was predicted using RNA folding Form software (http://mfold.rna.albany.edu/?q=mfold/RNA-Folding-Form).…”

Section: Bioinformatics Analysis and Statistical Analysismentioning

confidence: 99%

“…Based on the transcriptome data of L. vannamei (38), the target of miR-1959 was bioinformatically predicted by RNAhybrid software. The results showed that miR-1959 was imperfectly complementary with the 2709-2733 bp region of the mRNA of the Cactus gene, the IkB homolog in L. vannamei, just within the 39UTR (Fig.…”

Section: Target Identification Of Mir-1959mentioning

confidence: 99%

A MicroRNA-Mediated Positive Feedback Regulatory Loop of the NF-κB Pathway in Litopenaeus vannamei

Zuo

Jia

Chen

et al. 2016

The Journal of Immunology

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In the evolutionarily conserved canonical NF-κB pathway, degradation of the NF-κB inhibitor IκB in the cytoplasmic NF-κB/IκB complex allows the liberated NF-κB to translocate into the nucleus to activate various target genes. The regulatory mechanism governing this process needs further investigation. In this study, a novel microRNA, temporarily named miR-1959, was first identified from an invertebrate Litopenaeus vannamei. miR-1959 targets the 3′-untranslated region of the IκB homolog Cactus gene and reduces the protein level of Cactus in vivo, whereas the NF-κB homolog Dorsal directly binds the miR-1959 promoter to activate its transcription. Therefore, miR-1959 mediates a positive feedback regulatory loop, in that Dorsal activates miR-1959 expression, and in turn, miR-1959 inhibits the expression of Cactus, further leading to enhanced activation of Dorsal. Moreover, miR-1959 regulates the expression of many antimicrobial peptides in vivo and is involved in antibacterial immunity. To our knowledge, it is the first discovery of a microRNA-mediated feedback loop that directly regulates the NF-κB/IκB complex. This positive feedback loop could collaborate with the known NF-κB/IκB negative loop to generate a dynamic balance to regulate the activity of NF-κB, thus constituting an effective regulatory mechanism at the critical node of the NF-κB pathway.

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Analysis of Litopenaeus vannamei Transcriptome Using the Next-Generation DNA Sequencing Technique

Cited by 118 publications

References 54 publications

Transcriptome sequencing and analysis of the coconut leaf beetle, Brontispa longissima

Transcriptome sequencing and analysis of the coconut leaf beetle, Brontispa longissima

Crustacean hematopoiesis

A MicroRNA-Mediated Positive Feedback Regulatory Loop of the NF-κB Pathway in Litopenaeus vannamei

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