https://www.cell.com/trends/plant-science/pdf/S1360-1385(06)00248-2.pdf

The ABC's of comparative genomics in the Brassicaceae: building blocks of crucifer genomes

Brassica species include both vegetable and oilseed crops, which are very important to the daily life of common human beings. Meanwhile, the Brassica species represent an excellent system for studying numerous aspects of plant biology, specifically for the analysis of genome evolution following polyploidy, so it is also very important for scientific research. Now, the genome of Brassica rapa has already been assembled, it is the time to do deep mining of the genome data.

/pdf/brad-the-genetics-and-genomics-database-for-brassica-plants-34vdcpmpfq.pdf

BRAD, the genetics and genomics database for Brassica plants

Oilseed rape (Brassica napus) was selected as an example of a polyploid crop, and the Solexa sequencing system was used to generate approximately 20 million expressed sequence tags (ESTs) from each of two cultivars: Tapidor and Ningyou 7. A methodology and computational tools were developed to exploit, as a reference sequence, a publicly available set of approximately 94,000 Brassica species unigenes. Sequences transcribed in the leaves of juvenile plants were aligned to approximately 26 Mb of the reference sequences. The aligned sequences enabled the detection of 23,330-41,593 putative single nucleotide polymorphisms (SNPs) between the cultivars, depending on the read depth stringency applied. The majority of the detected polymorphisms (87.5-91.2%) were of a type indicative of transcription from homoeologous genes from the two parental genomes within oilseed rape, and are termed here 'hemi-SNPs'. The overall estimated polymorphism rate (approximately 0.047%-0.084%) is consistent with that previously observed between the cultivars analysed. To demonstrate the heritability of SNPs and to assess their suitability for applications such as linkage map construction and association genetics, approximately nine million ESTs were generated, using the Solexa system, from each of four lines of a doubled haploid mapping population derived from a cross between Tapidor and Ningyou 7. Computational tools were developed to score the alleles present in these lines for each of the potential SNPs identified between their parents. For a specimen region of the genome analysed in detail, segregation of alleles largely, although not entirely, followed the pattern expected for genomic markers.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1467-7652.2008.00396.x

Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing

Sequencing a genome and identifying genetic markers lays the groundwork for genome-wide association studies, but can be difficult to achieve for polyploid species. Harper et al. present an approach for performing association studies using genetic maps and markers generated from transcriptome sequencing data alone and apply it to the polyploid crop Brassica napus.

Associative transcriptomics of traits in the polyploid crop species Brassica napus.

All crop plants are polyploid and some genomes have been duplicated more recently than others. Advancements in cytogenetic and molecular tools, including high-density genetic mapping, fl orescent in situ hybridization, and genome and EST sequencing, have enabled new insights into genome composition and the history of genome duplications in crop plants. We review this evidence and discuss the relevance of genome duplication to crop improvement. Polyploidy provides genome buffering, increased allelic diversity and heterozygosity, and permits novel phenotypic variation to be generated. Polyploid formation is often accompanied with loss of duplicated chromatin, changes in gene expression, novel epistatic interactions, and endosperm effects. All of these factors need be considered in a genome-wide context for optimizing marker assisted selection and crop plant improvement. Abbreviations: Ks, synonymous sites; FLC, FLOWERING LOCUS C.

Polyploidy and Crop Improvement

Strong evidence exists for polyploidy having occurred during the evolution of the tribe Brassiceae. We show evidence for the dynamic and ongoing diploidization process by comparative analysis of the sequences of four paralogous Brassica rapa BAC clones and the homologous 124-kb segment of Arabidopsis thaliana chromosome 5. We estimated the times since divergence of the paralogous and homologous lineages. The three paralogous subgenomes of B. rapa triplicated 13 to 17 million years ago (MYA), very soon after the Arabidopsis and Brassica divergence occurred at 17 to 18 MYA. In addition, a pair of BACs represents a more recent segmental duplication, which occurred ∼0.8 MYA, and provides an exception to the general expectation of three paralogous segments within the B. rapa genome. The Brassica genome segments show extensive interspersed gene loss relative to the inferred structure of the ancestral genome, whereas the Arabidopsis genome segment appears little changed. Representatives of all 32 genes in the Arabidopsis genome segment are represented in Brassica, but the hexaploid complement of 96 has been reduced to 54 in the three subgenomes, with compression of the genomic region lengths they occupy to between 52 and 110 kb. The gene content of the recently duplicated B. rapa genome segments is identical, but intergenic sequences differ.

/pdf/sequence-level-analysis-of-the-diploidization-process-in-the-5ee5s55xkx.pdf

Sequence-Level Analysis of the Diploidization Process in the Triplicated FLOWERING LOCUS C Region of Brassica rapa

The marine mollusk Aplysia is a useful model organism for studying the cellular bases of behavior and plasticity. However, molecular studies of Aplysia have been limited by the lack of genomic information. Recently, a large scale characterization of neuronal transcripts was performed in A. californica. Here, we report the analysis of a parallel set of neuronal transcripts from a closely related species A. kurodai found in the northwestern Pacific. We collected 4,859 nonredundant sequences from the nervous system tissue of A. kurodai. By performing microarray and real-time PCR analyses, we found that ApC/EBP, matrilin, antistasin, and eIF3e clones were significantly up-regulated and a BAT1 homologous clone was significantly down-regulated by 5-HT treatment. Among these, we further demonstrated that the Ap-eIF3e plays a key role in 5-HT-induced long-term facilitation (LTF) as a positive regulator.

https://www.pnas.org/content/pnas/105/47/18602.full.pdf

Chang-Bae Kim

Papers

Sequence-Level Analysis of the Diploidization Process in the Triplicated FLOWERING LOCUS C Region of Brassica rapa

Transcriptome analysis and identification of regulators for long-term plasticity in Aplysia kurodai