The large yellow croaker, Larimichthys crocea is an important marine fish in China with a high economic value. In the last decade, the stock conservation and aquaculture industry of this species have been facing sever...The large yellow croaker, Larimichthys crocea is an important marine fish in China with a high economic value. In the last decade, the stock conservation and aquaculture industry of this species have been facing severe challenges because of wild population collapse and degeneration of important economic traits. However, genes contributing to growth and immunity in L. crocea have not been thoroughly analyzed, and available molecular markers are still not sufficient for genetic resource management and molecular selection. In this work, we sequenced the transcriptome in L. eroeea liver tissue with a Roche 454 sequencing platform and assembled the transcriptome into 93 801 transcripts. Of them, 38 856 transcripts were successfully annotated in nt, nr, Swiss-Prot, InterPro, COG, GO and KEGG databases. Based on the annotation information, 3 165 unigenes related to growth and immunity were identified. Additionally, a total of 6 391 simple sequence repeats （SSRs） were identified from the transcriptome, among which 4 498 SSRs had enough flanking regions to design primers for polymerase chain reactions （PCR）. To access the polymorphism of these markers, 30 primer pairs were randomly selected for PCR amplification and validation in 30 individuals, and 12 primer pairs （40.0%） exhibited obvious length polymorphisms. This work applied RNA-Seq to assemble and analyze a live transeriptome in L. crocea. With gene annotation and sequence information, genes related to growth and immunity were identified and massive SSR markers were developed, providing valuable genetic resources for future gene functional analysis and selective breeding ofL. eroeea.展开更多
Verticillium wilt disease becomes a major threat to many economically important crops. It is unclear whether and how plant immunity takes place during cotton-Verticillium interaction due to the lack of marker genes. T...Verticillium wilt disease becomes a major threat to many economically important crops. It is unclear whether and how plant immunity takes place during cotton-Verticillium interaction due to the lack of marker genes. Taking advantage of cotton （Gossypium hirsutum） genome, we discovered pathogenesis-related （PR） gene families, which have been widely used as markers of immune responses in plants. To profile the expression of G. hirsutum PR genes in the process of plant immunity, we treated cotton roots with two immunogenic peptides, fig22 and nlp20 known as pathogen-associated molecular patterns, as well as three Verticillium dahliae-derived peptides, nlp20vd2, nlp23vd3, and nlp23vd4 which are highly identical to nlp20. Quantitative real-time PCR results revealed that 14 G. hirsutum PR gene （GhPR） families were induced or suppressed independently in response to fig22, nip20, nlp20va2, nlp23vd3, and nlp23vd4. Most GhPR genes are expressed highest at 3 h post incubation of immunogenic peptides. Compared to fig22 and nlp20, nlp20vd2 is more effective to trigger up-regulated expression of GhPR genes. Notably, both nlp23vd3 and nlp23vd4 are able to induce GhPR gene up-regulation, although they do not induce necrosis on cotton leaves. Thus, our results provide marker genes and new immunogenic peptides for further investigation of cotton-V, dahliae interaction.展开更多
基金Supported by the National Natural Science Foundation of China(Nos.U1205122,31172397)the Key Project of Agricultural Science and Technology of Fujian Province(No.2011N5010)the Foundation for Innovation Research Team of Jimei University(No.2010A02)
文摘The large yellow croaker, Larimichthys crocea is an important marine fish in China with a high economic value. In the last decade, the stock conservation and aquaculture industry of this species have been facing severe challenges because of wild population collapse and degeneration of important economic traits. However, genes contributing to growth and immunity in L. crocea have not been thoroughly analyzed, and available molecular markers are still not sufficient for genetic resource management and molecular selection. In this work, we sequenced the transcriptome in L. eroeea liver tissue with a Roche 454 sequencing platform and assembled the transcriptome into 93 801 transcripts. Of them, 38 856 transcripts were successfully annotated in nt, nr, Swiss-Prot, InterPro, COG, GO and KEGG databases. Based on the annotation information, 3 165 unigenes related to growth and immunity were identified. Additionally, a total of 6 391 simple sequence repeats （SSRs） were identified from the transcriptome, among which 4 498 SSRs had enough flanking regions to design primers for polymerase chain reactions （PCR）. To access the polymorphism of these markers, 30 primer pairs were randomly selected for PCR amplification and validation in 30 individuals, and 12 primer pairs （40.0%） exhibited obvious length polymorphisms. This work applied RNA-Seq to assemble and analyze a live transeriptome in L. crocea. With gene annotation and sequence information, genes related to growth and immunity were identified and massive SSR markers were developed, providing valuable genetic resources for future gene functional analysis and selective breeding ofL. eroeea.
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB11040500) to Hui-Shan GuoNational Natural Science Foundation(31500119) to Chenlei HuaNational Natural Science Foundation(31600124) to Jian-Hua Zhao
文摘Verticillium wilt disease becomes a major threat to many economically important crops. It is unclear whether and how plant immunity takes place during cotton-Verticillium interaction due to the lack of marker genes. Taking advantage of cotton （Gossypium hirsutum） genome, we discovered pathogenesis-related （PR） gene families, which have been widely used as markers of immune responses in plants. To profile the expression of G. hirsutum PR genes in the process of plant immunity, we treated cotton roots with two immunogenic peptides, fig22 and nlp20 known as pathogen-associated molecular patterns, as well as three Verticillium dahliae-derived peptides, nlp20vd2, nlp23vd3, and nlp23vd4 which are highly identical to nlp20. Quantitative real-time PCR results revealed that 14 G. hirsutum PR gene （GhPR） families were induced or suppressed independently in response to fig22, nip20, nlp20va2, nlp23vd3, and nlp23vd4. Most GhPR genes are expressed highest at 3 h post incubation of immunogenic peptides. Compared to fig22 and nlp20, nlp20vd2 is more effective to trigger up-regulated expression of GhPR genes. Notably, both nlp23vd3 and nlp23vd4 are able to induce GhPR gene up-regulation, although they do not induce necrosis on cotton leaves. Thus, our results provide marker genes and new immunogenic peptides for further investigation of cotton-V, dahliae interaction.
