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

Characteristics of Asian honey bee (A. cerana) lincRNAs. a Length distribution of lincRNAs and mRNAs. b Distribution of exon number in lincRNAs and mRNAs. c Percentage of lincRNAs and mRNAs showing tissue-specific expression. d Heatmap showing expression levels of all lincRNAs (including the 464 tissue-specific lincRNAs, with a cutoff of a two-fold change identified by EdgeR) and e mRNAs based on FPKM in seven tissues (brain, antenna, hypoharyngeal gland, gut, fat body, larvae and venom gland)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig3: Characteristics of Asian honey bee (A. cerana) lincRNAs. a Length distribution of lincRNAs and mRNAs. b Distribution of exon number in lincRNAs and mRNAs. c Percentage of lincRNAs and mRNAs showing tissue-specific expression. d Heatmap showing expression levels of all lincRNAs (including the 464 tissue-specific lincRNAs, with a cutoff of a two-fold change identified by EdgeR) and e mRNAs based on FPKM in seven tissues (brain, antenna, hypoharyngeal gland, gut, fat body, larvae and venom gland)

Mentions: To investigate the basic features of A. cerana lincRNAs, we compared them with protein-coding mRNAs annotated in the Asian honey bee genome project [41]. Most (84 %) of the lincRNAs consisted of a single exon (Fig. 3b), while mRNAs had exon numbers ranging from 1 to over 16. The average length of lincRNA exons was 1232 bp, which is less than that of protein-coding exons. The majority of lincRNAs (over 85 %) were shorter than 2 kb, with very few (3 %) longer than 3 kb (Fig. 3a). The proportion of lincRNAs ranging from 1 to 2 kb was similar to that of mRNAs. Repetitive analysis was also performed to make a global view of repeat contents in honeybee lncRNAs. We found a low amount of repetitive content in the A. cerana lincRNA dataset. We identified as few as 33 retroelements, of which 3 elements were LINEs and 85 were LTR elements. In addition, we identified a total of 16 DNA transposons. On the whole, simple repeats were abundant (2743) compared to the other repetitive elements in lincRNAs. When we aligned the A. cerana lincRNAs with those from other species using BLAST with an e-value cutoff of 1E-03, we found detectable sequence similarity to 101 (4.0 %) lincRNAs from D. melanogaster, 176 (7.1 %) from C. elegans, 65 (2.6 %) from chicken, 217 (8.7 %) from cow, and 144 (5.8 %) from human.Fig. 3


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 Asian honey bee (A. cerana) lincRNAs. a Length distribution of lincRNAs and mRNAs. b Distribution of exon number in lincRNAs and mRNAs. c Percentage of lincRNAs and mRNAs showing tissue-specific expression. d Heatmap showing expression levels of all lincRNAs (including the 464 tissue-specific lincRNAs, with a cutoff of a two-fold change identified by EdgeR) and e mRNAs based on FPKM in seven tissues (brain, antenna, hypoharyngeal gland, gut, fat body, larvae and venom gland)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig3: Characteristics of Asian honey bee (A. cerana) lincRNAs. a Length distribution of lincRNAs and mRNAs. b Distribution of exon number in lincRNAs and mRNAs. c Percentage of lincRNAs and mRNAs showing tissue-specific expression. d Heatmap showing expression levels of all lincRNAs (including the 464 tissue-specific lincRNAs, with a cutoff of a two-fold change identified by EdgeR) and e mRNAs based on FPKM in seven tissues (brain, antenna, hypoharyngeal gland, gut, fat body, larvae and venom gland)
Mentions: To investigate the basic features of A. cerana lincRNAs, we compared them with protein-coding mRNAs annotated in the Asian honey bee genome project [41]. Most (84 %) of the lincRNAs consisted of a single exon (Fig. 3b), while mRNAs had exon numbers ranging from 1 to over 16. The average length of lincRNA exons was 1232 bp, which is less than that of protein-coding exons. The majority of lincRNAs (over 85 %) were shorter than 2 kb, with very few (3 %) longer than 3 kb (Fig. 3a). The proportion of lincRNAs ranging from 1 to 2 kb was similar to that of mRNAs. Repetitive analysis was also performed to make a global view of repeat contents in honeybee lncRNAs. We found a low amount of repetitive content in the A. cerana lincRNA dataset. We identified as few as 33 retroelements, of which 3 elements were LINEs and 85 were LTR elements. In addition, we identified a total of 16 DNA transposons. On the whole, simple repeats were abundant (2743) compared to the other repetitive elements in lincRNAs. When we aligned the A. cerana lincRNAs with those from other species using BLAST with an e-value cutoff of 1E-03, we found detectable sequence similarity to 101 (4.0 %) lincRNAs from D. melanogaster, 176 (7.1 %) from C. elegans, 65 (2.6 %) from chicken, 217 (8.7 %) from cow, and 144 (5.8 %) from human.Fig. 3

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