Transcriptome Analysis of the Chrysanthemum Foliar Nematode, Aphelenchoides ritzemabosi (Aphelenchida: Aphelenchoididae)

Abstract

The chrysanthemum foliar nematode (CFN), Aphelenchoides ritzemabosi, is a plant parasitic nematode that attacks many plants. In this study, a transcriptomes of mixed-stage population of CFN was sequenced on the Illumina HiSeq 2000 platform. 68.10 million Illumina high quality paired end reads were obtained which generated 26,817 transcripts with a mean length of 1,032 bp and an N50 of 1,672 bp, of which 16,467 transcripts were annotated against six databases. In total, 20,311 coding region sequences (CDS), 495 simple sequence repeats (SSRs) and 8,353 single-nucleotide polymorphisms (SNPs) were predicted, respectively. The CFN with the most shared sequences was B. xylophilus with 16,846 (62.82%) common transcripts and 10,543 (39.31%) CFN transcripts matched sequences of all of four plant parasitic nematodes compared. A total of 111 CFN transcripts were predicted as homologues of 7 types of carbohydrate-active enzymes (CAZymes) with plant/fungal cell wall-degrading activities, fewer transcripts were predicted as homologues of plant cell wall-degrading enzymes than fungal cell wall-degrading enzymes. The phylogenetic analysis of GH5, GH16, GH43 and GH45 proteins between CFN and other organisms showed CFN and other nematodes have a closer phylogenetic relationship. In the CFN transcriptome, sixteen types of genes orthologues with seven classes of protein families involved in the RNAi pathway in C. elegans were predicted. This research provides comprehensive gene expression information at the transcriptional level, which will facilitate the elucidation of the molecular mechanisms of CFN and the distribution of gene functions at the macro level, potentially revealing improved methods for controlling CFN.

Life-stage specific transcriptomes of a migratory endoparasitic plant nematode, Radopholus similis elucidate a different parasitic and life strategy of plant parasitic nematodes

“…GH, glycoside hydrolases; PL, polysaccharide lyases; EXPN, expansin-like proteins. The data of other nematodes come from previously reports 10–12,15–17 .…”

“…cDNA libraries of four life stages of R. similis were constructed as described previously 17 . These four libraries were sequenced by Illumina HiSeq™ 2000 (TruSeq SBS KIT-HS V3, Illumina).…”

“…These four libraries were sequenced by Illumina HiSeq™ 2000 (TruSeq SBS KIT-HS V3, Illumina). Data assembly and annotations were performed as described previously 17 . The full details of cDNA library construction, sequencing, data assembly used in this research were present in the Supporting Methods section in File S1.…”

“…Transcriptome analysis of PPNs can help us to know more about the biochemical and molecular processes of nematode development, reproduction and interaction with plant host, and to excavate pathogenic genes effectively. Recently, transcriptome data have been obtained from many PPNs 8–17 . Transcriptome sequencing had also been performed in R. similis using SMART cDNA synthesis method 18 .…”

Transcriptional responses of wheat and the cereal cyst nematode Heterodera avenae during their early contact stage

“…Studies on plant-nematode interactions have taken advantage of high-throughput techniques such as transcriptome sequencing, e.g., RKN 21 – 27 , cyst nematodes 28 – 34 and other PPNs 24 , 35 . The first de novo transcriptomic analysis compared the gene expression of pre-parasitic infective juveniles (J2s) to adults in H. avenae , which resulted in the identification of some important genes that may be involved in either plant parasitism or nematode metabolism 30 .…”