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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.


The expression abundance of microRNAs detected by real time RT-PCR (bars) and by high-throughput sequencing (lines).
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pone.0133491.g005: The expression abundance of microRNAs detected by real time RT-PCR (bars) and by high-throughput sequencing (lines).

Mentions: We selected 5 microRNAs for validation using RT-PCR, including 3 known microRNAs and 2 novel microRNAs of M. incognita. All of the 5 microRNAs could be detected using real time RT-PCR with the mature microRNAs as a primer. The microRNA expression was determined using real time RT-PCR by 2-ΔCt measurements. The expression levels of four microRNAs, miR-71, miR-100b, NOVEL-1 and NOVEL-2, were consistent with those obtained by high-throughput sequencing. The expression levels of miR-71 and miR-100b were much higher than those of NOVEL-1 and NOVEL-2 in both results of sequencing and qRT-PCR. However, the expression abundance of let-7 detected by real time RT-PCR is much higher than that by high-throughput sequencing (Fig 5).


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)

The expression abundance of microRNAs detected by real time RT-PCR (bars) and by high-throughput sequencing (lines).
© Copyright Policy
Related In: Results  -  Collection

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

pone.0133491.g005: The expression abundance of microRNAs detected by real time RT-PCR (bars) and by high-throughput sequencing (lines).
Mentions: We selected 5 microRNAs for validation using RT-PCR, including 3 known microRNAs and 2 novel microRNAs of M. incognita. All of the 5 microRNAs could be detected using real time RT-PCR with the mature microRNAs as a primer. The microRNA expression was determined using real time RT-PCR by 2-ΔCt measurements. The expression levels of four microRNAs, miR-71, miR-100b, NOVEL-1 and NOVEL-2, were consistent with those obtained by high-throughput sequencing. The expression levels of miR-71 and miR-100b were much higher than those of NOVEL-1 and NOVEL-2 in both results of sequencing and qRT-PCR. However, the expression abundance of let-7 detected by real time RT-PCR is much higher than that by high-throughput sequencing (Fig 5).

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.