| Oxya chinensis is one of the main pests at the rice production area in China. They mainly feed on leaves and grain of rice, and also damage graminoid plants such as wheat, corn, beans et al. In recent years, with the adjustment of agricultural planting form, winter climate warming, ecological environment changes and many other factors, O. chinensis has become the main pest in the rice production area of the middle and lower reaches of Yangtze River. It has caused a huge economic loss to our agriculture. At present, physiological and biochemical characteristics, life history, ecological distribution and mitochondrial genome of O.chinensis have been studied, but has not report about genome and transcriptome of O. chinensis.The genome of Locusts is not yet available because of its large size (about6500Mb), it is nearly2times larger than the human genome and36times larger than the genome of Drosophila melanogaster. However, the transcriptome of Locusts has a relatively small amount of data, and through the high-throughput sequencing, we can get the effective information about gene expression and regulation in the whole genome range. Therefore, in this study, transcriptome of O. chinensis (both nymph and adult) had been sequenced in the normal condition by Illumina HiSeq2000high-throughput sequencing platform. We analysed large amounts of sequencing data by the bioinformatics method, and found many differentially expressed genes between nymph and adult. It can accumulate abundant data information for pest management. At the same time, O. chinensis’s mitochondrial genome transcriptional map was constructed, with which can overcome the shortage when annotating mitochondrial genome using bioinformatics method.The main results drawn from this study are as follows:(1) Two cDNA libraries (nymph and adult) of O. chinensis were built, and sequenced use the HiSeq2000sequencing platform. Each sample generated4G data, the nymph generated59,940,260raw reads, the adult generated58,428,216raw reads. Because of the genome of O. chinensis remains unknown, we obtained152,974nymph Contig and134,352adult Contig through de novo assembly. Further assembly yeiled76,924nymph Unigenes and66,794adult Unigenes. Nymph has10,130Unigenes more than the adult, it means that in the growth phase, the nymph need to synthesize more proteins related to growth. Therefore, the transcription level of the nymph was significantly higher than that of the adult. At last, Unigenes of the two samples were clustering joining together, finally we obtained68,166Unigenes of O. chinensis with an average length of599bp.(2) According to the theory that" Sequence similar, the same as its function", the68,166Unigenes blasted against various protein databases, totally27,933Unigenes can be annotated by Nr、KEGG、 COG、 GO databases, about40%the total Unigenes of O. chinensis. In GO,6,439annotated Unigenes which had homology were classed into three categories. Most of them were involved in biological process, such as cell processes, metabolic processes and so on. As for molecular function, most of annotated Unigenes were involved in binding (all kinds of connection form) and activity (including all kinds of catalytic enzyme, transcription regulation factor, protein receptors activity).(3) In KEGG Pathway analysis of All-Unigene,18,020Unigenes involved in242metabolic or signaling pathways. We found12Unigenes related to TAP, and a series of Unigenes related to eIFs.91Unigenes involved in insect hormone biosynthesis, including juvenile hormone, ecdysone, steroid hormone and sex pheromone. The discovery of these genes will lay sufficient foundation for the development of O. chinensis hormone pesticide.(4)65,535of the total68,166O. chinensis Unigenes were differentially expressed genes based on the RPKM value. Among them,20,044were up-regulated and45,491were down-regulated.(5) We selected14,648significantly differentially expressed genes (DEGs) from65,535genes whose expression level is different between the nymph and the adult (FDR<0.001, fold-change>2).5,378Unigenes were assigned to GO functional classification,2,575involved in biological process,1,700involved in cellular component,1,103were annotated into molecular function. Most genes were annotated into function of activity、regulation and cell. KEGG Pathway analysis of DEGs show that3,577Unigenes involved in236metabolic or signaling pathways. Genes that are related to reproductive metabolic pathways, regulation and control of circadian rhythm-fly, nucleotide replication and transcription, protein translation and modification, phosphatidylinositol signaling system et al. are all up-regulated or down-regulated in the different degree. It shows that these genes play an important role in the growth and development, physiological rhythms of O. chinensis. (6) Through mitochondrial transcript mapping, we analysed mitochondrial transcripts of O. chinensis, and found that expression level of two rRNA genes are higher in the nymph, and transcriptional efficiency of rRNA is higher than protein coding genes. O. chinensis have5large transcriptional units. Overlap genes ATP6/ATP8、ND4/ND4L are transcribed in a bicistronic mRNA respectively, whose3’-end are Polyadenylation. The coverage of ND2、COX1、COX2、ATP6/ATP8、COX3、 ND3and CYTB are higher, and they should be mature transcripts. Some region of ND5、NDD4、ND4L and ND1are almost not covered, these genes are coding NADH dehydrogenase in the light chain. They are the key enzyme of mitochondrial oxidative phosphorylation, so we inferred that dues to a lower detection when sequencing or by different stability of the transcripts. Post-transcriptional regulation of gene expression play a key role in mitochondrial transcript modification, and it is mainly reflected in change of the protein abundance is higher than mRNA. |
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