Small RNA Sequencing Reveals Regulatory Roles of MicroRNAs in the Development of Meloidogyne incognita.

Huawei Liu,Li Qiu,Runrun Sun,Baohong Zhang,Robert L Nichols,Xiaoping Pan

doi:10.3390/ijms20215466

Abstract

MicroRNAs (miRNAs) are an extensive class of small regulatory RNAs. Knowing the specific expression and functions of miRNAs during root-knot nematode (RKN) (Meloidogyne incognita) development could provide fundamental information about RKN development as well as a means to design new strategies to control RKN infection, a major problem of many important crops. Employing high throughput deep sequencing, we identified a total of 45 conserved and novel miRNAs from two developmental stages of RKN, eggs and J2 juveniles, during their infection of cotton (Gossypium hirsutum L.). Twenty-one of the miRNAs were differentially expressed between the two stages. Compared with their expression in eggs, two miRNAs were upregulated (miR252 and miRN19), whereas 19 miRNAs were downregulated in J2 juveniles. Nine miRNAs were expressed at high levels, with >1000 reads per mapped million (RPM) sequenced reads in both eggs and J2 juveniles (miR1, miR124, miR2-3p, miR252, miR279, miR57-5p, miR7904, miR87, and miR92). Three miRNAs were only expressed in eggs (miR4738, miRN3, and miRN5). These differentially expressed miRNAs may control RKN development by regulating specific protein-coding genes in pathways associated with RKN growth and development.

Highlights

Parasitic nematodes are pests affecting crop yields and quality in many important crops such as cotton (Gossypium hirsutum L.), the most economically significant fiber crop
All small RNAs from M. incognita obtained at the two developmental stages were sequenced
A total of 19,952,271 and 17,526,380 reads were obtained for the egg and J2 juvenile stages, respectively

Summary

Introduction

Parasitic nematodes are pests affecting crop yields and quality in many important crops such as cotton (Gossypium hirsutum L.), the most economically significant fiber crop. The most damaging nematode parasites in the U.S cotton crop are root-knot (Meloidogyne incognita), reniform (Rotylenchulus reniformis), and sting (Belonolaimus longicaudatus) nematodes [1]. Infection of M. incognita to plant roots is intimately involved in its life-cycle. The infective second-stage juvenile (J2) enters plant roots and migrates to the vascular tissues, where it transforms certain vascular cells into multinucleate and hypertrophied so-termed “giant cells”, which become the nematodes’ feeding and reproduction sites. To transform and maintain the giant cells, the nematodes secrete effector proteins into the plants via the stylet in their mouth parts [2,3,4]. The nematode will become sedentary, use the giant cells as feeding sites, go through J3 and J4 molts, and develop into a reproductive female which will lay thousands of eggs. Some genes coding for the effector proteins that facilitate parasitism have been identified [6]; the regulation of such gene expression remains unclear

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Results

Conclusion