Limits...
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

Differential expression of virus-specific lincRNAs. Relative expression of lincRNAs between uninfected (Control) and SBV- and DWV-infected bees. Quantitative analysis was carried out using StepOne plus Software V. 2.0 (Applied Biosystems). Results were normalized to a validated control gene, actin (data not shown), for which values were set to 1, using the ΔΔCt method for each sample [58]. SBV- and DWV-infected samples were collected from A. cerana and A. mellifera, respectively
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig5: Differential expression of virus-specific lincRNAs. Relative expression of lincRNAs between uninfected (Control) and SBV- and DWV-infected bees. Quantitative analysis was carried out using StepOne plus Software V. 2.0 (Applied Biosystems). Results were normalized to a validated control gene, actin (data not shown), for which values were set to 1, using the ΔΔCt method for each sample [58]. SBV- and DWV-infected samples were collected from A. cerana and A. mellifera, respectively

Mentions: Additionally, we examined the responses of these lincRNAs to other viral diseases in the honey bee to investigate if they are specific to SBV. DWV, a viral disease closely linked to Varroa mite infestation [52], causes wing deformity and premature death in adult honey bees of A. mellifera [52]. Hence, we investigated the expression patterns of those same 11 lincRNAs in DWV-infected and healthy uninfected A. mellifera honey bees using qRT-PCR. Intriguingly, we found that 10 of the lincRNAs showed a similar expression pattern in response to infection in this species, including the one down-regulated (AC_lincRNA.3472.1; Fig. 5). Furthermore, RT-PCR products for 10 lincRNAs from A. cerana were sequenced and found to match exactly to those lincRNAs (Additional file 5: Dataset S3). Together, these results suggest that this subset of 10 lincRNAs may play critical roles in pathogen-host interactions in honey bees. Therefore we regarded these lincRNAs as virus-specific lincRNAs in honey bee. We have submitted these virus-specific lincRNAs to GenBank (Acc. Nos.: KM889914-KM889923).Fig. 5


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)

Differential expression of virus-specific lincRNAs. Relative expression of lincRNAs between uninfected (Control) and SBV- and DWV-infected bees. Quantitative analysis was carried out using StepOne plus Software V. 2.0 (Applied Biosystems). Results were normalized to a validated control gene, actin (data not shown), for which values were set to 1, using the ΔΔCt method for each sample [58]. SBV- and DWV-infected samples were collected from A. cerana and A. mellifera, respectively
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig5: Differential expression of virus-specific lincRNAs. Relative expression of lincRNAs between uninfected (Control) and SBV- and DWV-infected bees. Quantitative analysis was carried out using StepOne plus Software V. 2.0 (Applied Biosystems). Results were normalized to a validated control gene, actin (data not shown), for which values were set to 1, using the ΔΔCt method for each sample [58]. SBV- and DWV-infected samples were collected from A. cerana and A. mellifera, respectively
Mentions: Additionally, we examined the responses of these lincRNAs to other viral diseases in the honey bee to investigate if they are specific to SBV. DWV, a viral disease closely linked to Varroa mite infestation [52], causes wing deformity and premature death in adult honey bees of A. mellifera [52]. Hence, we investigated the expression patterns of those same 11 lincRNAs in DWV-infected and healthy uninfected A. mellifera honey bees using qRT-PCR. Intriguingly, we found that 10 of the lincRNAs showed a similar expression pattern in response to infection in this species, including the one down-regulated (AC_lincRNA.3472.1; Fig. 5). Furthermore, RT-PCR products for 10 lincRNAs from A. cerana were sequenced and found to match exactly to those lincRNAs (Additional file 5: Dataset S3). Together, these results suggest that this subset of 10 lincRNAs may play critical roles in pathogen-host interactions in honey bees. Therefore we regarded these lincRNAs as virus-specific lincRNAs in honey bee. We have submitted these virus-specific lincRNAs to GenBank (Acc. Nos.: KM889914-KM889923).Fig. 5

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