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Identification of MicroRNAs in Meloidogyne incognita Using Deep Sequencing.

Wang Y, Mao Z, Yan J, Cheng X, Liu F, Xiao L, Dai L, Luo F, Xie B - PLoS ONE (2015)

Bottom Line: We found that four microRNAs, miR-100, miR-92, miR-279 and miR-137, exist only in genomes of parasitic nematodes, but do not exist in the genomes of the free living nematode C. elegans.Our research created a unique resource for the research of plant parasitic nematodes.The candidate microRNAs could help elucidate the genomic structure, gene regulation, evolutionary processes, and developmental features of plant parasitic nematodes and nematode-plant interaction.

View Article: PubMed Central - PubMed

Affiliation: Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, PR China; Institute of Vegetables and Flowers, CAAS, Beijing, PR China.

ABSTRACT
MicroRNAs play important regulatory roles in eukaryotic lineages. In this paper, we employed deep sequencing technology to sequence and identify microRNAs in M. incognita genome, which is one of the important plant parasitic nematodes. We identified 102 M. incognita microRNA genes, which can be grouped into 71 nonredundant miRNAs based on mature sequences. Among the 71 miRANs, 27 are known miRNAs and 44 are novel miRNAs. We identified seven miRNA clusters in M. incognita genome. Four of the seven clusters, miR-100/let-7, miR-71-1/miR-2a-1, miR-71-2/miR-2a-2 and miR-279/miR-2b are conserved in other species. We validated the expressions of 5 M. incognita microRNAs, including 3 known microRNAs (miR-71, miR-100b and let-7) and 2 novel microRNAs (NOVEL-1 and NOVEL-2), using RT-PCR. We can detect all 5 microRNAs. The expression levels of four microRNAs obtained using RT-PCR were consistent with those obtained by high-throughput sequencing except for those of let-7. We also examined how M. incognita miRNAs are conserved in four other nematodes species: C. elegans, A. suum, B. malayi and P. pacificus. We found that four microRNAs, miR-100, miR-92, miR-279 and miR-137, exist only in genomes of parasitic nematodes, but do not exist in the genomes of the free living nematode C. elegans. Our research created a unique resource for the research of plant parasitic nematodes. The candidate microRNAs could help elucidate the genomic structure, gene regulation, evolutionary processes, and developmental features of plant parasitic nematodes and nematode-plant interaction.

No MeSH data available.


Size distribution of reads from microRNA, protein encoding genes and others.
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pone.0133491.g002: Size distribution of reads from microRNA, protein encoding genes and others.

Mentions: To annotate the small RNAs, we aligned the clean reads against the microRNAs, tRNA, rRNA, snRNA and mRNA sequences of M. incognita and then counted the reads of each class. There were 74.35%, 5.38% and 1.10% of clean reads mapped to predicted microRNA, protein encoding and tRNA genes, respectively. There were 19.14% of clean reads mapped to other classes, including rRNA, snRNA, and siRNA (Fig 1B). There were 9.4% of clean reads that were unable to be mapped to the M. incognita genome with no mismatches. The top 10 most abundance sequence tags were all microRNAs. The lengths of the microRNA reads were mainly distributed between 18 and 23 nt, which include 86.34% of the total microRNA reads (Fig 2).


Identification of MicroRNAs in Meloidogyne incognita Using Deep Sequencing.

Wang Y, Mao Z, Yan J, Cheng X, Liu F, Xiao L, Dai L, Luo F, Xie B - PLoS ONE (2015)

Size distribution of reads from microRNA, protein encoding genes and others.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4524723&req=5

pone.0133491.g002: Size distribution of reads from microRNA, protein encoding genes and others.
Mentions: To annotate the small RNAs, we aligned the clean reads against the microRNAs, tRNA, rRNA, snRNA and mRNA sequences of M. incognita and then counted the reads of each class. There were 74.35%, 5.38% and 1.10% of clean reads mapped to predicted microRNA, protein encoding and tRNA genes, respectively. There were 19.14% of clean reads mapped to other classes, including rRNA, snRNA, and siRNA (Fig 1B). There were 9.4% of clean reads that were unable to be mapped to the M. incognita genome with no mismatches. The top 10 most abundance sequence tags were all microRNAs. The lengths of the microRNA reads were mainly distributed between 18 and 23 nt, which include 86.34% of the total microRNA reads (Fig 2).

Bottom Line: We found that four microRNAs, miR-100, miR-92, miR-279 and miR-137, exist only in genomes of parasitic nematodes, but do not exist in the genomes of the free living nematode C. elegans.Our research created a unique resource for the research of plant parasitic nematodes.The candidate microRNAs could help elucidate the genomic structure, gene regulation, evolutionary processes, and developmental features of plant parasitic nematodes and nematode-plant interaction.

View Article: PubMed Central - PubMed

Affiliation: Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, PR China; Institute of Vegetables and Flowers, CAAS, Beijing, PR China.

ABSTRACT
MicroRNAs play important regulatory roles in eukaryotic lineages. In this paper, we employed deep sequencing technology to sequence and identify microRNAs in M. incognita genome, which is one of the important plant parasitic nematodes. We identified 102 M. incognita microRNA genes, which can be grouped into 71 nonredundant miRNAs based on mature sequences. Among the 71 miRANs, 27 are known miRNAs and 44 are novel miRNAs. We identified seven miRNA clusters in M. incognita genome. Four of the seven clusters, miR-100/let-7, miR-71-1/miR-2a-1, miR-71-2/miR-2a-2 and miR-279/miR-2b are conserved in other species. We validated the expressions of 5 M. incognita microRNAs, including 3 known microRNAs (miR-71, miR-100b and let-7) and 2 novel microRNAs (NOVEL-1 and NOVEL-2), using RT-PCR. We can detect all 5 microRNAs. The expression levels of four microRNAs obtained using RT-PCR were consistent with those obtained by high-throughput sequencing except for those of let-7. We also examined how M. incognita miRNAs are conserved in four other nematodes species: C. elegans, A. suum, B. malayi and P. pacificus. We found that four microRNAs, miR-100, miR-92, miR-279 and miR-137, exist only in genomes of parasitic nematodes, but do not exist in the genomes of the free living nematode C. elegans. Our research created a unique resource for the research of plant parasitic nematodes. The candidate microRNAs could help elucidate the genomic structure, gene regulation, evolutionary processes, and developmental features of plant parasitic nematodes and nematode-plant interaction.

No MeSH data available.