ArticleBMC plant biology2015
Digital gene expression analysis of gene expression differences within Brassica diploids and allopolyploids.
Article in BMC plant biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed, 34 citations in OpenAlex.
- Functional and regulatory diversity of homeobox-leucine zipper transcription factors BnaHB6 under dehydration and salt stress in Brassica napus L.Plant molecular biology · 2024Article
- Analysis of Transcriptional Changes in DifferentGenes · 2021Article
- Genome-wide analysis of alternative splicing divergences between Brassica hexaploid and its parents.Planta · 2019Article
- Genome-wide identification and characterization of abiotic-stress responsive SOD (superoxide dismutase) gene family in Brassica juncea and B. rapa.BMC genomics · 2019Article
- Article
- Genomic and transcriptomic alterations following intergeneric hybridization and polyploidization in theHorticulture research · 2018Article
- Down-regulation of BnDA1, whose gene locus is associated with the seeds weight, improves the seeds weight and organ size in Brassica napus.Plant biotechnology journal · 2017Article
- A comparative study of the seed structure between resynthesized allotetraploid and their diploid parents.Protoplasma · 2017Article
- Digital Gene Expression Analysis Provides Insight into the Transcript Profile of the Genes Involved in Aporphine Alkaloid Biosynthesis in Lotus (Frontiers in plant science · 2017Article
- Epiallelic changes in known stress-responsive genes under extreme drought conditions in Brassica juncea (L.) Czern.Plant cell reports · 2017Article
- Digital Gene Expression Profiling to Explore Differentially Expressed Genes Associated with Terpenoid Biosynthesis during Fruit Development in Litsea cubeba.Molecules (Basel, Switzerland) · 2016Article
- Review
- Identification, duplication, evolution and expression analyses of caleosins in Brassica plants and Arabidopsis subspecies.Molecular genetics and genomics : MGG · 2016Article
- Intracellular Ca(2+) and K(+) concentration in Brassica oleracea leaf induces differential expression of transporter and stress-related genes.BMC genomics · 2016Article
- Genome-Wide Gene Expressions Respond Differently to A-subgenome Origins inFrontiers in plant science · 2016Article
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundBrassica includes many successfully cultivated crop species of polyploid origin, either by ancestral genome triplication or by hybridization between two diploid progenitors, displaying complex repetitive sequences and transposons. The U's triangle, which consists of three diploids and three amphidiploids, is optimal for the analysis of complicated genomes after polyploidization. Next-generation sequencing enables the transcriptome profiling of polyploids on a global scale.
resultsWe examined the gene expression patterns of three diploids (Brassica rapa, B. nigra, and B. oleracea) and three amphidiploids (B. napus, B. juncea, and B. carinata) via digital gene expression analysis. In total, the libraries generated between 5.7 and 6.1 million raw reads, and the clean tags of each library were mapped to 18547-21995 genes of B. rapa genome. The unambiguous tag-mapped genes in the libraries were compared. Moreover, the majority of differentially expressed genes (DEGs) were explored among diploids as well as between diploids and amphidiploids. Gene ontological analysis was performed to functionally categorize these DEGs into different classes. The Kyoto Encyclopedia of Genes and Genomes analysis was performed to assign these DEGs into approximately 120 pathways, among which the metabolic pathway, biosynthesis of secondary metabolites, and peroxisomal pathway were enriched. The non-additive genes in Brassica amphidiploids were analyzed, and the results indicated that orthologous genes in polyploids are frequently expressed in a non-additive pattern. Methyltransferase genes showed differential expression pattern in Brassica species.
conclusionOur results provided an understanding of the transcriptome complexity of natural Brassica species. The gene expression changes in diploids and allopolyploids may help elucidate the morphological and physiological differences among Brassica species.
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