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Genome-wide identification of long noncoding RNA genes and their potential association with fecundity and virulence in rice brown planthopper, Nilaparvata lugens.

Xiao H, Yuan Z, Guo D, Hou B, Yin C, Zhang W, Li F - BMC Genomics (2015)

Bottom Line: Three lncRNAs specifically expressed in HFP and LFP populations overlapped with reproductive-associated genes.This study provided the first catalog of lncRNA genes in rice brown planthopper.Gene expression and genome location analysis indicated that lncRNAs might play important roles in high fecundity and virulence adaptation in N. lugens.

View Article: PubMed Central - PubMed

Affiliation: Department of Entomology, College of Plant protection, Nanjing Agricultural University, Nanjing, 210095, China.

ABSTRACT

Background: The functional repertoire of long noncoding RNA (lncRNA) has been characterized in several model organisms, demonstrating that lncRNA plays important roles in fundamental biological processes. However, they remain largely unidentified in most species. Understanding the characteristics and functions of lncRNA in insects would be useful for insect resources utilization and sustainable pest control.

Methods: A computational pipeline was developed to identify lncRNA genes in the rice brown planthopper, Nilaparvata lugens, a destructive rice pest causing huge yield losses. Strand specific RT-PCR were used to determine the transcription orientation of lncRNAs.

Results: In total, 2,439 lncRNA transcripts corresponding to 1,882 loci were detected from 12 whole transcriptomes (RNA-seq) datasets, including samples from high fecundity (HFP), low fecundity (LFP), I87i and C89i populations, in addition Mudgo and TN1 virulence strains. The identified N. lugens lncRNAs had low sequence similarities with other known lncRNAs. However, their structural features were similar with mammalian counterparts. N. lugens lncRNAs had shorter transcripts than protein-coding genes due to the lower exon number though their exons and introns were longer. Only 19.9% of N. lugens lncRNAs had multiple alternatively spliced isoforms. We observed biases in the genome location of N. lugens lncRNAs. More than 30% of the lncRNAs overlapped with known protein-coding genes. These lncRNAs tend to be co-expressed with their neighboring genes (Pearson correlation, p < 0.01, T-test) and might interact with adjacent protein-coding genes. In total, 19-148 lncRNAs were specifically-expressed in the samples of HFP, LFP, Mudgo, TN1, I87i and C89i populations. Three lncRNAs specifically expressed in HFP and LFP populations overlapped with reproductive-associated genes.

Discussion: The structural features of N. lugens lncRNAs are similar to mammalian counterparts. Coexpression and function analysis suggeste that N. lugens lncRNAs might have important functions in high fecundity and virulence adaptability.

Conclusions: This study provided the first catalog of lncRNA genes in rice brown planthopper. Gene expression and genome location analysis indicated that lncRNAs might play important roles in high fecundity and virulence adaptation in N. lugens.

No MeSH data available.


Related in: MedlinePlus

Exon and intron structures of three lncRNA genes that were specifically expressed in the HFP or LFP population. These lncRNAs overlapped with reproduction-associated protein genes encoding glucose dehydrogenase, gastrulation defective, and GALNT7. F: Forward primer, R: Reverse primer
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Fig10: Exon and intron structures of three lncRNA genes that were specifically expressed in the HFP or LFP population. These lncRNAs overlapped with reproduction-associated protein genes encoding glucose dehydrogenase, gastrulation defective, and GALNT7. F: Forward primer, R: Reverse primer

Mentions: We found that three lncRNA genes overlapped with reproduction-associated genes (Fig. 10). Two lncRNAs (BPHOGS10035598-OT and BPHOGS100007976-OT) were specifically-expressed in the fifth instar nymph of the HFP population. One lncRNA (BPHOGS10005591-OT2) was specifically-expressed in the fifth instar nymph of the LFP population. BPHOGS10005591-OT2 overlapped with the glucose dehydrogenase (GLD) gene at the 3′ region comprising 2365 bp. GLD is essential for sperm storage in adult female of D. melanogaster. BPHOGS100007976-OT was located at the 5′-upstream of the gastrulation defective gene and overlapped with this gene for 3354 bp. The gastrulation defective gene encodes a serine protease that cleaves and activates protein SNAKE. The activated SNAKE cleaves and activates protein EASTER. This series of activations controls the embryo dorsoventral polarity. BPHOGS10035598-OT overlapped with the N-acetylgalactosaminytransferase 7 gene (GALNT7) at its 5′-end for 878 bp. GALNT7 participates in reproductive regulation in D. melanogaster.Fig. 10


Genome-wide identification of long noncoding RNA genes and their potential association with fecundity and virulence in rice brown planthopper, Nilaparvata lugens.

Xiao H, Yuan Z, Guo D, Hou B, Yin C, Zhang W, Li F - BMC Genomics (2015)

Exon and intron structures of three lncRNA genes that were specifically expressed in the HFP or LFP population. These lncRNAs overlapped with reproduction-associated protein genes encoding glucose dehydrogenase, gastrulation defective, and GALNT7. F: Forward primer, R: Reverse primer
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4594746&req=5

Fig10: Exon and intron structures of three lncRNA genes that were specifically expressed in the HFP or LFP population. These lncRNAs overlapped with reproduction-associated protein genes encoding glucose dehydrogenase, gastrulation defective, and GALNT7. F: Forward primer, R: Reverse primer
Mentions: We found that three lncRNA genes overlapped with reproduction-associated genes (Fig. 10). Two lncRNAs (BPHOGS10035598-OT and BPHOGS100007976-OT) were specifically-expressed in the fifth instar nymph of the HFP population. One lncRNA (BPHOGS10005591-OT2) was specifically-expressed in the fifth instar nymph of the LFP population. BPHOGS10005591-OT2 overlapped with the glucose dehydrogenase (GLD) gene at the 3′ region comprising 2365 bp. GLD is essential for sperm storage in adult female of D. melanogaster. BPHOGS100007976-OT was located at the 5′-upstream of the gastrulation defective gene and overlapped with this gene for 3354 bp. The gastrulation defective gene encodes a serine protease that cleaves and activates protein SNAKE. The activated SNAKE cleaves and activates protein EASTER. This series of activations controls the embryo dorsoventral polarity. BPHOGS10035598-OT overlapped with the N-acetylgalactosaminytransferase 7 gene (GALNT7) at its 5′-end for 878 bp. GALNT7 participates in reproductive regulation in D. melanogaster.Fig. 10

Bottom Line: Three lncRNAs specifically expressed in HFP and LFP populations overlapped with reproductive-associated genes.This study provided the first catalog of lncRNA genes in rice brown planthopper.Gene expression and genome location analysis indicated that lncRNAs might play important roles in high fecundity and virulence adaptation in N. lugens.

View Article: PubMed Central - PubMed

Affiliation: Department of Entomology, College of Plant protection, Nanjing Agricultural University, Nanjing, 210095, China.

ABSTRACT

Background: The functional repertoire of long noncoding RNA (lncRNA) has been characterized in several model organisms, demonstrating that lncRNA plays important roles in fundamental biological processes. However, they remain largely unidentified in most species. Understanding the characteristics and functions of lncRNA in insects would be useful for insect resources utilization and sustainable pest control.

Methods: A computational pipeline was developed to identify lncRNA genes in the rice brown planthopper, Nilaparvata lugens, a destructive rice pest causing huge yield losses. Strand specific RT-PCR were used to determine the transcription orientation of lncRNAs.

Results: In total, 2,439 lncRNA transcripts corresponding to 1,882 loci were detected from 12 whole transcriptomes (RNA-seq) datasets, including samples from high fecundity (HFP), low fecundity (LFP), I87i and C89i populations, in addition Mudgo and TN1 virulence strains. The identified N. lugens lncRNAs had low sequence similarities with other known lncRNAs. However, their structural features were similar with mammalian counterparts. N. lugens lncRNAs had shorter transcripts than protein-coding genes due to the lower exon number though their exons and introns were longer. Only 19.9% of N. lugens lncRNAs had multiple alternatively spliced isoforms. We observed biases in the genome location of N. lugens lncRNAs. More than 30% of the lncRNAs overlapped with known protein-coding genes. These lncRNAs tend to be co-expressed with their neighboring genes (Pearson correlation, p < 0.01, T-test) and might interact with adjacent protein-coding genes. In total, 19-148 lncRNAs were specifically-expressed in the samples of HFP, LFP, Mudgo, TN1, I87i and C89i populations. Three lncRNAs specifically expressed in HFP and LFP populations overlapped with reproductive-associated genes.

Discussion: The structural features of N. lugens lncRNAs are similar to mammalian counterparts. Coexpression and function analysis suggeste that N. lugens lncRNAs might have important functions in high fecundity and virulence adaptability.

Conclusions: This study provided the first catalog of lncRNA genes in rice brown planthopper. Gene expression and genome location analysis indicated that lncRNAs might play important roles in high fecundity and virulence adaptation in N. lugens.

No MeSH data available.


Related in: MedlinePlus