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Genome-wide characterization of long intergenic non-coding RNAs (lincRNAs) provides new insight into viral diseases in honey bees Apis cerana and Apis mellifera.

Jayakodi M, Jung JW, Park D, Ahn YJ, Lee SC, Shin SY, Shin C, Yang TJ, Kwon HW - BMC Genomics (2015)

Bottom Line: Long non-coding RNAs (lncRNAs) are a class of RNAs that do not encode proteins.A total of 863 (57 %) and 464 (18 %) lincRNAs showed tissue-dependent expression in A. mellifera and A. cerana, respectively, most preferentially in ovary and fat body tissues.This study provides the first comprehensive set of lincRNAs for honey bees and opens the door to discover lincRNAs associated with biological and hormone signaling pathways as well as various diseases of honey bee.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. murukarthick@snu.ac.kr.

ABSTRACT

Background: Long non-coding RNAs (lncRNAs) are a class of RNAs that do not encode proteins. Recently, lncRNAs have gained special attention for their roles in various biological process and diseases.

Results: In an attempt to identify long intergenic non-coding RNAs (lincRNAs) and their possible involvement in honey bee development and diseases, we analyzed RNA-seq datasets generated from Asian honey bee (Apis cerana) and western honey bee (Apis mellifera). We identified 2470 lincRNAs with an average length of 1011 bp from A. cerana and 1514 lincRNAs with an average length of 790 bp in A. mellifera. Comparative analysis revealed that 5 % of the total lincRNAs derived from both species are unique in each species. Our comparative digital gene expression analysis revealed a high degree of tissue-specific expression among the seven major tissues of honey bee, different from mRNA expression patterns. A total of 863 (57 %) and 464 (18 %) lincRNAs showed tissue-dependent expression in A. mellifera and A. cerana, respectively, most preferentially in ovary and fat body tissues. Importantly, we identified 11 lincRNAs that are specifically regulated upon viral infection in honey bees, and 10 of them appear to play roles during infection with various viruses.

Conclusions: This study provides the first comprehensive set of lincRNAs for honey bees and opens the door to discover lincRNAs associated with biological and hormone signaling pathways as well as various diseases of honey bee.

No MeSH data available.


Related in: MedlinePlus

Schematic diagram of the bioinformatics pipeline for lincRNA prediction. Step-wise in silico filtration of lincRNAs is shown for both A. mellifera and A. cerana
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Fig1: Schematic diagram of the bioinformatics pipeline for lincRNA prediction. Step-wise in silico filtration of lincRNAs is shown for both A. mellifera and A. cerana

Mentions: To identify a comprehensive set of Asian honey bee lincRNAs, we used Illumina RNA-seq data generated for the A. cerana genome project [41] (for six tissues: antenna, brain, hypoharyngeal gland, gut, fat body, and venom gland) and newly generated datasets from larvae, and Sacbrood virus (SBV)-infected and non-infected honey bees (Table 1). We established a bioinformatics pipeline by modifying protocols used in various previous studies [34, 48, 49] (Fig. 1). A reference-guided assembly yielded a total of 24,529 transcripts from 18,937 gene loci. The assembled sequences were analyzed to identify putative lncRNAs, and 19,916 transcripts were selected based on nucleotide length ≥200 bp and ORF ≤ 100 amino acids (Fig. 1). We chose not to consider the protein-coding transcripts in order to increase the accuracy in identifying lncRNAs. From the filtered transcripts, we removed transcripts with overlapping Swiss-Prot protein sequences (http://www.uniprot.org/). The remaining 9373 transcripts were filtered based on coding potential evaluation, removing those with scores ≤ −1.0 using the Coding Potential Calculator (CPC) program, which is a state-of-the-art tool for assessing protein coding potential [50]. It is also necessary to remove pseudogenes and other classes of RNAs such as tRNAs, rRNAs and snRNAs to avoid misprediction. Accordingly, we established a housekeeping RNA database (see Methods) for similarity-based elimination and obtained 8715 putative long non-coding transcripts after removing housekeeping RNAs (Fig. 1). Further, transcripts derived from the mitochondrial genome were filtered by similarity searches against A. cerana mitochondrial protein sequences. After applying all these criteria, we identified 7376 candidate loci to encode 7969 putative lncRNAs.Table 1


Genome-wide characterization of long intergenic non-coding RNAs (lincRNAs) provides new insight into viral diseases in honey bees Apis cerana and Apis mellifera.

Jayakodi M, Jung JW, Park D, Ahn YJ, Lee SC, Shin SY, Shin C, Yang TJ, Kwon HW - BMC Genomics (2015)

Schematic diagram of the bioinformatics pipeline for lincRNA prediction. Step-wise in silico filtration of lincRNAs is shown for both A. mellifera and A. cerana
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4559890&req=5

Fig1: Schematic diagram of the bioinformatics pipeline for lincRNA prediction. Step-wise in silico filtration of lincRNAs is shown for both A. mellifera and A. cerana
Mentions: To identify a comprehensive set of Asian honey bee lincRNAs, we used Illumina RNA-seq data generated for the A. cerana genome project [41] (for six tissues: antenna, brain, hypoharyngeal gland, gut, fat body, and venom gland) and newly generated datasets from larvae, and Sacbrood virus (SBV)-infected and non-infected honey bees (Table 1). We established a bioinformatics pipeline by modifying protocols used in various previous studies [34, 48, 49] (Fig. 1). A reference-guided assembly yielded a total of 24,529 transcripts from 18,937 gene loci. The assembled sequences were analyzed to identify putative lncRNAs, and 19,916 transcripts were selected based on nucleotide length ≥200 bp and ORF ≤ 100 amino acids (Fig. 1). We chose not to consider the protein-coding transcripts in order to increase the accuracy in identifying lncRNAs. From the filtered transcripts, we removed transcripts with overlapping Swiss-Prot protein sequences (http://www.uniprot.org/). The remaining 9373 transcripts were filtered based on coding potential evaluation, removing those with scores ≤ −1.0 using the Coding Potential Calculator (CPC) program, which is a state-of-the-art tool for assessing protein coding potential [50]. It is also necessary to remove pseudogenes and other classes of RNAs such as tRNAs, rRNAs and snRNAs to avoid misprediction. Accordingly, we established a housekeeping RNA database (see Methods) for similarity-based elimination and obtained 8715 putative long non-coding transcripts after removing housekeeping RNAs (Fig. 1). Further, transcripts derived from the mitochondrial genome were filtered by similarity searches against A. cerana mitochondrial protein sequences. After applying all these criteria, we identified 7376 candidate loci to encode 7969 putative lncRNAs.Table 1

Bottom Line: Long non-coding RNAs (lncRNAs) are a class of RNAs that do not encode proteins.A total of 863 (57 %) and 464 (18 %) lincRNAs showed tissue-dependent expression in A. mellifera and A. cerana, respectively, most preferentially in ovary and fat body tissues.This study provides the first comprehensive set of lincRNAs for honey bees and opens the door to discover lincRNAs associated with biological and hormone signaling pathways as well as various diseases of honey bee.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. murukarthick@snu.ac.kr.

ABSTRACT

Background: Long non-coding RNAs (lncRNAs) are a class of RNAs that do not encode proteins. Recently, lncRNAs have gained special attention for their roles in various biological process and diseases.

Results: In an attempt to identify long intergenic non-coding RNAs (lincRNAs) and their possible involvement in honey bee development and diseases, we analyzed RNA-seq datasets generated from Asian honey bee (Apis cerana) and western honey bee (Apis mellifera). We identified 2470 lincRNAs with an average length of 1011 bp from A. cerana and 1514 lincRNAs with an average length of 790 bp in A. mellifera. Comparative analysis revealed that 5 % of the total lincRNAs derived from both species are unique in each species. Our comparative digital gene expression analysis revealed a high degree of tissue-specific expression among the seven major tissues of honey bee, different from mRNA expression patterns. A total of 863 (57 %) and 464 (18 %) lincRNAs showed tissue-dependent expression in A. mellifera and A. cerana, respectively, most preferentially in ovary and fat body tissues. Importantly, we identified 11 lincRNAs that are specifically regulated upon viral infection in honey bees, and 10 of them appear to play roles during infection with various viruses.

Conclusions: This study provides the first comprehensive set of lincRNAs for honey bees and opens the door to discover lincRNAs associated with biological and hormone signaling pathways as well as various diseases of honey bee.

No MeSH data available.


Related in: MedlinePlus