生物
龙葵
小桶
转录组
WRKY蛋白质结构域
基因
遗传学
候选基因
参考基因组
Illumina染料测序
植物
基因组
基因表达
作者
Kinjal Kulshrestha,Akarsh Parihar,Pratibha Parihar
出处
期刊:Plant Gene
[Elsevier]
日期:2020-12-01
卷期号:24: 100255-100255
被引量:7
标识
DOI:10.1016/j.plgene.2020.100255
摘要
The present work includes the transcriptome analysis of tomato genotypes namely AT-3 (S. lycopersicum), SL 120 (S. lycopersicum), LA 1777 (S. habrochaites) and LA 2157 (S. arcanum) under nematode, M. incognita stress. The sequencing done on Illumina MiSeq platform yielded 5.24 Gb of raw data. Overall alignment with reference sequences of Solanum lycopersicum assembly SL3.0 was 85.60% and with M. incognita V3 was 9.80%. AT-3 (S. lycopersicum), SL 120 (S. lycopersicum), LA 1777 (S. habrochaites) and LA 2157 (S. arcanum) aligned with tomato reference genome with a similarity of 75.37%, 82.05%, 73.04% and 69.24% respectively. BlastX result showed that 80.76% of blasted sequences were mapped and 73.07% were annotated. Maximum sequences (94%) were mapped with UniProtKB. Top Blast hit was for S. lycopersicum followed by S. pennellii. Highest evidence code distribution was for IEA (Inferred from Electronic Annotation). The highest enzyme code distribution was found for hydrolases. Gene ontology was found for defense response, response to stress, response to fungus and response to biotic stimulus. PC1 captured 41.3% of variance and PC2 represented 31.2%. Differential gene expression was noted for chitinase activity, PAL, SAM, BURP and peroxidases. All the transcripts of nematode infected tomato had 85 KEGG pathways. Validation of defense related genes through real-time PCR was done for genes of chitinase, pathogenesis related, LeHSP, SAM, LYC WRKY and MYB TF.
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