- Genome-wide analysis of long non-coding RNAs in adult tissues of the melon fly,. - Information on lncRNA in the melon fly, Zeugodacus cucurbitae (Coquillett) is currently limited.. - Differentially expressed lncRNAs were analyzed between tissues, and. - Specifically expressed lncRNAs were identified and filtered in tissues of female and male Z. - Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of targets of midgut-specific lncRNAs indicated an enrichment of the metabolic process.. - Conclusions: This was the first systematic identification of lncRNA in the melon fly. - Keywords: Long non-coding RNA, Zeugodacus cucurbitae, RNA-seq, Transcriptome, Differential expressions. - Hundreds of insect genomes and transcriptomes are now accessible in the NCBI Short Read Archive (SRA) database. - As the member of the non-coding RNA families, long non-coding RNA (lncRNA) is defined as. - In eukary- otes, lncRNAs are transcribed at several sites of the. - The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. - If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. - 1 Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, China Full list of author information is available at the end of the article. - In Drosophila, lncRNAs were probable involved in molting because the mass of lncRNAs was significantly up- regulated in the late embryonic and larval stages [5].. - Knockdown of lincRNA_1317 expression by RNA interfer- ence suppressed the replication of dengue virus in Aedes aegypti, demonstrating the essential role of the lncRNA in anti-viral defenses [24]. - Functional annotation of target genes of testis-specific lncRNAs from RNA-seq data indicated that they may participate in the spermatogenesis of Bombyx mori [26].. - Tissue-specific lncRNAs were screened in female and male tissues based on their relative expression levels.. - Q30 scores were ≥ 93.0% in all of the samples. - base was detected in any of the samples (Table 1). - All of the RNA sequencing data produced in this study are avail- able in the NCBI BioProject database (http://www.ncbi.. - In fe- males, the largest population of lncRNAs (1024) was found in the Malpighian tubules (Fig. - After discarding all null-expressed lncRNAs, a total of 3124 lncRNA tran- scripts were strictly identified from the transcriptome data of the eight tissues. - Most of the lncRNAs in Z. - Expression of lncRNAs in Z . - A total of 151 higher- and 103 lower- expressed lncRNAs were found in the comparison of Malpighian tubules vs. - Tissue-specific lncRNAs were identified in all tissues.. - A total of 42 ovary-specific lncRNAs had a relatively high expression in the ovary compared with other female tissues (Fig. - A total of 457 target genes were obtained in the female midgut, among which 51 were cis-regulated and 410 were trans-regulated. - For the male midgut, a total of 273 target genes were predicted, including 34 Table 1 Summary statistics of the RNA-seq data. - Four differentially expressed lncRNAs were randomly se- lected and their expression patterns in the eight tissues were examined by RT-qPCR. - “N” base was detected in any of the samples. - It is pos- sible that the presence of microbes in the Z. - cucurbitae midgut resulted in the relatively low genome mapping rates. - A low mapping rate was also reported in the mid- gut transcriptome of mosquito [38]. - After identification under a computational pipeline, the screening criteria of the expression threshold of at least 1 FPKM in each tis- sue resulted in a strict catalog containing 3124 lncRNAs.. - A similar result was reported in Drosophila, in which 1077 lncRNAs were identified from 43,967 transcripts in the transcriptomes of different development stages [5].. - Differences in the lncRNA numbers of different tissues may explain the variable lncRNA amounts in different insect species. - lincRNA means long intergenic non-coding RNA. - In Drosophila, lincRNAs and sense lncRNAs were present in the largest and smallest numbers, respectively [39], which was consistent with our results. - In the melon fly, the lengths of lncRNA transcripts were variable. - Each section of the Venn diagrams shows the numbers of differentially expressed lncRNAs with a ratio of two tissues expression level above 10. - 6 GO and KEGG pathway analyses of the target genes of midgut-specific lncRNAs in Zeugodacus cucurbitae. - a GO analysis of the functions of lncRNA target genes. - Tissue-specific lncRNAs were obtained in female and male tissues of Z. - Drosophila transcriptome analysis re- vealed that many lncRNAs had dominant expression in the testis [18], which was similar to our findings. - This verifies the high quality of the RNA-seq [13].. - In Apis melli- fera, over-expression of an ovary-specific lncRNAs lncov1 during a critical developmental period revealed its potential roles in regulating the ovary size of the. - mori, functional annotation of Malpighian tubules-specific lncRNAs indicated integral components of membrane and oxidative phosphoryl- ation were abundantly annotated, and fat body-specific lncRNAs suggested enrichment of the oxidation- reduction process and metabolic pathways [26]. - Similarly, in Anopheles gambiae, metab- olism was enriched in the functional annotation of lncRNA targets from the transcriptome of the midgut [44]. - Thus, metabolism was enriched in midgut-specific lncRNA targets, indicating unique functions of the mid- gut and serving as a guideline for further functional research.. - Tissue-specific lncRNAs were identified in female and. - The bar represents the mean lncRNA expression and the error bar represents the positive standard error (SE) of the mean. - A Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI, USA) was used to remove rRNA in the input mater- ial, which contained 1.5 μg RNA per sample. - NEBNext Adaptor was ligated with a hairpin loop struc- ture to prepare for hybridization after adenylation of the. - 3′-ends of the sequence fragments. - A total of 3 μL of USER Enzyme (NEB) was used in the procedure of size-selected and adaptor-ligated cDNA at 37 °C for 15 min. - In the end, an AMPure XP system (Beckman Coulter) was implemented in purification of PCR products, and evaluation of library quality was per- formed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA) [45]. - All of the downstream ana- lysis were performed with clean data. - Cufflinks (version and Scripture (versions VPaperR3) [48] software were used to assemble the final transcriptome, parameters “oper- ation core number 4, library-type fr-unstrande” were used in Cufflinks and all the other parameters were de- fault in the two softwares. - Identification of long non-coding RNAs. - In the first, transcripts shorter than 200 nt and those overlapped with protein-coding genes in the same sense of strand were discarded. - Tissue-specific lncRNAs refer to lncRNAs that have ex- tremely high expression in the given tissue [18]. - cucurbitae, DESeq was used to analyze the significance of the differential expression of lncRNAs in each two tis- sues [55]. - Two categories (cis-regulation and trans-regulation) of the lncRNA regulation modes were analyzed. - All of the identified cis- and trans- regulated protein-coding genes were used for GO and KEGG pathway analysis. - To validate expression patterns of differentially expressed lncRNAs, the eight tissues were dissected from 5-day-old melon fly adults in the same manner as the sequenced samples. - LincRNA: long intergenic non-coding RNA. - LncRNA: long non-coding RNA. - All of the authors have read and approved the final manuscript.. - All of the RNA sequencing data produced in the current study are available in the NCBI BioProject database (http://www.ncbi.nlm.nih.gov/bioproject/) under the accession number: PRJNA579200.. - Zeugodacus cucurbitae is one of the most common agricultural pests, which is not included in the “ List of Endangered and Protected Animals in China. - Genome-wide identification of long non-coding RNA genes and their association with insecticide resistance and metamorphosis in diamondback moth, Plutella xylostella. - Genome-wide identification of long non-coding RNAs and their regulatory networks involved in Apis mellifera ligustica response to Nosema ceranae infection. - Unique features of long non-coding RNA biogenesis and function. - On the classification of long non-coding RNAs. - Genome- wide identification and characterization of long non-coding RNAs in developmental skeletal muscle of fetal goat. - Dynamic expression of long non-coding RNAs (lncRNAs) in adult zebrafish. - A long non-coding RNA promotes full activation of adult gene expression in the chicken α -globin domain. - Genome-wide identification and functional prediction of long noncoding RNAs involved in the heat stress response in Metarhizium robertsii. - Diversity and dynamics of the Drosophila transcriptome. - Genome-wide identification and characterization of putative lncRNAs in the diamondback moth, Plutella xylostella (L. - Long non-coding RNAs: new players in cell differentiation and development. - Systematic identification and characterization of long non-coding RNAs in the silkworm, Bombyx mori. - Eradication of the melon fly, Bactrocera cucurbitae, in Japan: importance of behavior, ecology, genetics, and evolution. - Functional response of the pupal parasitoid, Dirhinus giffardii towards two fruit fly species, Bactrocera zonata and B. - A chromosome-scale assembly of the Bactrocera cucurbitae genome provides insight to the genetic basis of white pupae.. - Genome- wide gene expression profiling of the melon fly, Zeugodacus cucurbitae, during thirteen life stages. - Long non-coding RNAs regulating immunity in insects. - Non-coding RNA. - Genome-wide characterization and developmental expression profiling of long non-coding RNAs in Sogatella furcifera. - Non-coding RNAs: epigenetic regulators of bone development and homeostasis. - De novo assembly and sex-specific transcriptome profiling in the sand fly Phlebotomus perniciosus (Diptera, Phlebotominae), a major old world vector of Leishmania infantum. - Global analysis of small non-coding RNA populations across tissues in the malaria vector, Anopheles gambiae. - Integrating RNA-seq and ChIP-seq data to characterize long non- coding RNAs in Drosophila melanogaster. - Genome-wide identification of tissue- specific long non-coding RNA in three farm animal species. - The novel long non-coding RNA CRG regulates Drosophila locomotor behavior. - In depth annotation of the Anopheles gambiae mosquito midgut transcriptome. - accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. - Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. - Genomic and transcriptional co- localization of protein-coding and long non-coding RNA pairs in the developing brain
Xem thử không khả dụng, vui lòng xem tại trang nguồn hoặc xem
Tóm tắt