Limits...
Expression patterns, molecular markers and genetic diversity of insect-susceptible and resistant Barbarea genotypes by comparative transcriptome analysis.

Zhang X, Liu T, Wei X, Qiu Y, Song J, Wang H, Shen D, Agerbirk N, Li X - BMC Genomics (2015)

Bottom Line: However, gene expression for two downstream enzymes, the glucosyl transferase (UGT73C11) and an oxidosqualene cyclase (OSC), were significantly upregulated in the P-type compared with the G-type plant.The homologous genes from P- and G-type plants were detected by BLAST unigenes with a cutoff level E-value < e(-10). 12,980 gene families containing 26,793 P-type and 36,944 G-type unigenes were shared by the two types of B. vulgaris. 38,397 single nucleotide polymorphisms (SNPs) were found in 9,452 orthologous genes between the P- and G-type plants.These data represent useful information for pest-resistance gene mining and for the investigation of the molecular basis of plant-pest interactions.

View Article: PubMed Central - PubMed

Affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China. zhangxiaohui01@caas.cn.

ABSTRACT

Background: Barbarea vulgaris contains two genotypes: the glabrous type (G-type), which confers resistance to the diamondback moth (DBM) and other insect pests, and the pubescent type (P-type), which is susceptible to the DBM. Herein, the transcriptomes of P-type B. vulgaris before and after DBM infestation were subjected to Illumina (Solexa) pyrosequencing and comparative analysis.

Results: 5.0 gigabase pairs of clean nucleotides were generated. Non-redundant unigenes (33,721) were assembled and 94.1 % of them were annotated. Compared with our previous G-type transcriptome, the expression patterns of many insect responsive genes, including those related to secondary metabolism, phytohormones and transcription factors, which were significantly induced by DBM in G-type plants, were less sensitive to DBM infestation in P-type plants. The genes of the triterpenoid saponin pathway were identified in both G- and P-type plants. The upstream genes of the pathway showed similar expression patterns between the two genotypes. However, gene expression for two downstream enzymes, the glucosyl transferase (UGT73C11) and an oxidosqualene cyclase (OSC), were significantly upregulated in the P-type compared with the G-type plant. The homologous genes from P- and G-type plants were detected by BLAST unigenes with a cutoff level E-value < e(-10). 12,980 gene families containing 26,793 P-type and 36,944 G-type unigenes were shared by the two types of B. vulgaris. 38,397 single nucleotide polymorphisms (SNPs) were found in 9,452 orthologous genes between the P- and G-type plants. We also detected 5,105 simple sequence repeats (SSRs) in the B. vulgaris transcriptome, comprising mono-nucleotide-repeats (2,477; 48.5 %) and triple-nucleotide-repeats (1,590; 31.1 %). Of these, 1,657 SSRs displayed polymorphisms between the P- and G-type. Consequently, 913 SSR primer pairs were designed with a resolution of more than two nucleotides. We randomly chose 30 SSRs to detect the genetic diversity of 32 Barbarea germplasms. The distance tree showed that these accessions were clearly divided into groups, with the G-type grouping with available Western and Central European B. vulgaris accessions in contrast to the P-type accession, B. stricta and B. verna.

Conclusions: These data represent useful information for pest-resistance gene mining and for the investigation of the molecular basis of plant-pest interactions.

No MeSH data available.


Related in: MedlinePlus

Function classification of unigenes. a, The gene ontology (GO) classification of P-type B. vulgaris transcripts; b, The comparison of clusters of orthologous groups of proteins (COGs) classification between P- and G-type transcriptomes
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4487577&req=5

Fig1: Function classification of unigenes. a, The gene ontology (GO) classification of P-type B. vulgaris transcripts; b, The comparison of clusters of orthologous groups of proteins (COGs) classification between P- and G-type transcriptomes

Mentions: Subsequently, we screened the unigene sequences against the NCBI non-redundant (Nr), SwissProt, Gene Ontology (GO), Clusters of Orthologous Groups of proteins (COGs), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway protein databases using BLASTX (e-value < 0.00001). Protein function was predicted from the annotations of the most similar proteins in those databases. As shown in Table 1, 31,715 (94.1 %) unigenes were annotated by at least one of these databases. Detailed information on the Nt, Nr, SwissProt, GO, COGs and KEGG annotations is shown in Tables S2–S7, respectively. The gene functional classification by GO analysis showed that the largest GO terms were “cell”, “binding activity” and “physiological processes” from the “cellular component”, “molecular function” and “biological process” ontologies, respectively. The most abundant COGs terms were “general function prediction only”, “replication, recombination and repair” and “transcription”. The distributions of the functional categories were similar to that of G-type plants (Fig. 1).Fig. 1


Expression patterns, molecular markers and genetic diversity of insect-susceptible and resistant Barbarea genotypes by comparative transcriptome analysis.

Zhang X, Liu T, Wei X, Qiu Y, Song J, Wang H, Shen D, Agerbirk N, Li X - BMC Genomics (2015)

Function classification of unigenes. a, The gene ontology (GO) classification of P-type B. vulgaris transcripts; b, The comparison of clusters of orthologous groups of proteins (COGs) classification between P- and G-type transcriptomes
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4487577&req=5

Fig1: Function classification of unigenes. a, The gene ontology (GO) classification of P-type B. vulgaris transcripts; b, The comparison of clusters of orthologous groups of proteins (COGs) classification between P- and G-type transcriptomes
Mentions: Subsequently, we screened the unigene sequences against the NCBI non-redundant (Nr), SwissProt, Gene Ontology (GO), Clusters of Orthologous Groups of proteins (COGs), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway protein databases using BLASTX (e-value < 0.00001). Protein function was predicted from the annotations of the most similar proteins in those databases. As shown in Table 1, 31,715 (94.1 %) unigenes were annotated by at least one of these databases. Detailed information on the Nt, Nr, SwissProt, GO, COGs and KEGG annotations is shown in Tables S2–S7, respectively. The gene functional classification by GO analysis showed that the largest GO terms were “cell”, “binding activity” and “physiological processes” from the “cellular component”, “molecular function” and “biological process” ontologies, respectively. The most abundant COGs terms were “general function prediction only”, “replication, recombination and repair” and “transcription”. The distributions of the functional categories were similar to that of G-type plants (Fig. 1).Fig. 1

Bottom Line: However, gene expression for two downstream enzymes, the glucosyl transferase (UGT73C11) and an oxidosqualene cyclase (OSC), were significantly upregulated in the P-type compared with the G-type plant.The homologous genes from P- and G-type plants were detected by BLAST unigenes with a cutoff level E-value < e(-10). 12,980 gene families containing 26,793 P-type and 36,944 G-type unigenes were shared by the two types of B. vulgaris. 38,397 single nucleotide polymorphisms (SNPs) were found in 9,452 orthologous genes between the P- and G-type plants.These data represent useful information for pest-resistance gene mining and for the investigation of the molecular basis of plant-pest interactions.

View Article: PubMed Central - PubMed

Affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China. zhangxiaohui01@caas.cn.

ABSTRACT

Background: Barbarea vulgaris contains two genotypes: the glabrous type (G-type), which confers resistance to the diamondback moth (DBM) and other insect pests, and the pubescent type (P-type), which is susceptible to the DBM. Herein, the transcriptomes of P-type B. vulgaris before and after DBM infestation were subjected to Illumina (Solexa) pyrosequencing and comparative analysis.

Results: 5.0 gigabase pairs of clean nucleotides were generated. Non-redundant unigenes (33,721) were assembled and 94.1 % of them were annotated. Compared with our previous G-type transcriptome, the expression patterns of many insect responsive genes, including those related to secondary metabolism, phytohormones and transcription factors, which were significantly induced by DBM in G-type plants, were less sensitive to DBM infestation in P-type plants. The genes of the triterpenoid saponin pathway were identified in both G- and P-type plants. The upstream genes of the pathway showed similar expression patterns between the two genotypes. However, gene expression for two downstream enzymes, the glucosyl transferase (UGT73C11) and an oxidosqualene cyclase (OSC), were significantly upregulated in the P-type compared with the G-type plant. The homologous genes from P- and G-type plants were detected by BLAST unigenes with a cutoff level E-value < e(-10). 12,980 gene families containing 26,793 P-type and 36,944 G-type unigenes were shared by the two types of B. vulgaris. 38,397 single nucleotide polymorphisms (SNPs) were found in 9,452 orthologous genes between the P- and G-type plants. We also detected 5,105 simple sequence repeats (SSRs) in the B. vulgaris transcriptome, comprising mono-nucleotide-repeats (2,477; 48.5 %) and triple-nucleotide-repeats (1,590; 31.1 %). Of these, 1,657 SSRs displayed polymorphisms between the P- and G-type. Consequently, 913 SSR primer pairs were designed with a resolution of more than two nucleotides. We randomly chose 30 SSRs to detect the genetic diversity of 32 Barbarea germplasms. The distance tree showed that these accessions were clearly divided into groups, with the G-type grouping with available Western and Central European B. vulgaris accessions in contrast to the P-type accession, B. stricta and B. verna.

Conclusions: These data represent useful information for pest-resistance gene mining and for the investigation of the molecular basis of plant-pest interactions.

No MeSH data available.


Related in: MedlinePlus