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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

Characteristics of Western honey bee (A. mellifera) lincRNAs. a Length distribution of lincRNAs and mRNAs. b Distribution of exon number in lincRNAs and mRNAs. c Percentage of lincRNAs specifically expressed in various A. mellifera tissues
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Fig4: Characteristics of Western honey bee (A. mellifera) lincRNAs. a Length distribution of lincRNAs and mRNAs. b Distribution of exon number in lincRNAs and mRNAs. c Percentage of lincRNAs specifically expressed in various A. mellifera tissues

Mentions: Similar results were obtained for A. mellifera, in which many of the lincRNAs (77 %) consisted of a single exon (Fig. 4b) and the average length of lincRNAs (790 bp) was shorter than that of annotated protein-coding mRNAs (1266 bp). Similar to A. cerana, the majority of the A. mellifera lincRNAs were within 2 kb of genes (Fig. 3a), and approximately 18 % were distributed within 400 to 500 bp from a gene. The A. mellifera lincRNAs showed similarity to fewer than 2 % of the known lncRNAs from other species and were rich in simple repeats (1156). Annotation files describing the genomic features are available as Additional file 2: Dataset S1 and Additional file 3: Dataset S2; Table 2 shows a comparison of the sequence features of lincRNAs identified in this study. All lincRNAs identified in this study and their respective annotation information can be downloaded at http://mnbldb.snu.ac.kr/data.php.Fig. 4


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)

Characteristics of Western honey bee (A. mellifera) lincRNAs. a Length distribution of lincRNAs and mRNAs. b Distribution of exon number in lincRNAs and mRNAs. c Percentage of lincRNAs specifically expressed in various A. mellifera tissues
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig4: Characteristics of Western honey bee (A. mellifera) lincRNAs. a Length distribution of lincRNAs and mRNAs. b Distribution of exon number in lincRNAs and mRNAs. c Percentage of lincRNAs specifically expressed in various A. mellifera tissues
Mentions: Similar results were obtained for A. mellifera, in which many of the lincRNAs (77 %) consisted of a single exon (Fig. 4b) and the average length of lincRNAs (790 bp) was shorter than that of annotated protein-coding mRNAs (1266 bp). Similar to A. cerana, the majority of the A. mellifera lincRNAs were within 2 kb of genes (Fig. 3a), and approximately 18 % were distributed within 400 to 500 bp from a gene. The A. mellifera lincRNAs showed similarity to fewer than 2 % of the known lncRNAs from other species and were rich in simple repeats (1156). Annotation files describing the genomic features are available as Additional file 2: Dataset S1 and Additional file 3: Dataset S2; Table 2 shows a comparison of the sequence features of lincRNAs identified in this study. All lincRNAs identified in this study and their respective annotation information can be downloaded at http://mnbldb.snu.ac.kr/data.php.Fig. 4

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