A5075070162- Plant Disease Resistance and Genetics
- Genetic Mapping and Diversity in Plants and Animals
- RNA Research and Splicing
- Nitrogen and Sulfur Effects on Brassica
- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Plant Molecular Biology Research
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Molecular Biology Techniques and Applications
- Genomics and Rare Diseases
- Plant Pathogens and Fungal Diseases
- Research in Cotton Cultivation
- Photosynthetic Processes and Mechanisms
- Plant Reproductive Biology
- Genetic Neurodegenerative Diseases
- Microbial Natural Products and Biosynthesis
- Genetic and phenotypic traits in livestock
- Plant biochemistry and biosynthesis
- Mycorrhizal Fungi and Plant Interactions
- RNA and protein synthesis mechanisms
- Plant Gene Expression Analysis
Huazhong Agricultural University
2021-2025
Shanghai Zhangjiang Laboratory
2021
With the increasing availability of massive transcriptome data in plants, it is possible to construct a comprehensive database with multiple and online imputation tools. Online databases integrated, multifaceted functions for exploring published RNA-seq libraries or microarrays are available several plant species (Darwish et al., 2013; Xia 2017; Zhang 2020), helping researchers take advantage vast collection public sets. Brassica napus (AACC, 2n = 38) one most important oil crops,...
Abstract Cotton is an important economic crop, and many loci for traits have been identified, but it remains challenging time-consuming to identify candidate or causal genes/variants clarify their roles in phenotype formation regulation. Here, we first collected integrated the multi-omics datasets including 25 genomes, transcriptomes 76 tissue samples, epigenome data of five species metabolome 768 metabolites from four tissues, genetic variation, trait transcriptome 4180 cotton accessions....
Abstract Insertions are one of the major types structural variations and defined as addition 50 nucleotides or more into a DNA sequence. Several methods exist to detect insertions from next-generation sequencing short read data, but they generally have low sensitivity. Our contribution is two-fold. First, we introduce INSurVeyor, fast, sensitive precise method that detects paired-end data. Using publicly available benchmark datasets (both human non-human), show INSurVeyor not only than any...
Clubroot is one of the most important diseases for many cruciferous vegetables and oilseed crops worldwide. Different clubroot resistance (CR) loci have been identified from only limited species in Brassica, making it difficult to compare utilize these loci. European fodder turnip ECD04 considered valuable resources CR breeding. To explore genetic evolutionary basis ECD04, we sequenced genome using de novo assembly 978 candidate R genes. Subsequently, 28 published were physically mapped 15...
Although individual genomic structural variants (SVs) are known to influence gene expression and trait variation, the extent scale of SV impact across a species remain unknown. In present study, we constructed reference library 334,461 SVs from genome assemblies 16 representative morphotypes neopolyploid Brassica napus accessions detected 258,865 in 2,105 resequenced genomes. Coupling with 5 tissue population transcriptomes, uncovered 285,976 SV-expression quantitative loci (eQTLs) that...
The Solanaceae family, which includes economically important crops such as tomatoes, potatoes and peppers, has experienced a rapid expansion in genomic data due to advancements sequencing technologies. However, existing databases are limited by incomplete species representation, lack of comprehensive comparative tools the absence systematic pan-genomic analyses. To address these gaps, we developed Information Resource (SoIR, https://soir.bio2db.com), genomics database for family. SoIR...
Here, we describe the Herbivore Transcriptome Integrated Resource Database (HTIRDB, https://yanglab.hzau.edu.cn/HTIRDB#/). The HTIRDB comprises self-generated transcriptomic data from 100 to 105 tissues two female domestic herbivores six species (cattle, donkey, goat, horse, rabbit, and sika deer) breeds of sheep, an extra 28,710 related published datasets. user-friendly interface provides tools functionalities that facilitate exploration gene expression between species. for comparative...
Summary Plant hormones are the intrinsic factors that control plant development. The integration of different phytohormone pathways in a complex network synergistic, antagonistic and additive interactions has been elucidated model plants. However, systemic level transcriptional responses to hormone crosstalk Brassica napus is largely unknown. Here, we present an in‐depth temporal‐resolution study transcriptomes seven B. seedlings. Differentially expressed gene analysis revealed few common...
Large indels greatly impact the observable phenotypes in different organisms including plants and human. Hence, extracting large with high precision sensitivity is important. Here, we developed IndelEnsembler to detect 1047 Arabidopsis whole-genome sequencing data. identified 34 093 deletions, 12 913 tandem duplications 9773 insertions. Our indel dataset was more comprehensive accurate compared previous of AthCNV (1). We captured nearly twice ground truth deletions on average 27% AthCNV,...
As the largest family of dicotyledon, Asteraceae comprises a variety economically important crops, ornamental plants and numerous medicinal herbs. Advancements in genomics transcriptomic have revolutionized research species, generating extensive omics data that necessitate an efficient platform for integration analysis. However, existing databases face challenges mining genes with specific functions supporting cross-species studies. To address these gaps, we introduce Multi-omics Information...