We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. The B. rapa genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica oil and vegetable crops.

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The genome of the mesopolyploid crop species Brassica rapa

EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

/pdf/automated-eukaryotic-gene-structure-annotation-using-3fo28wpira.pdf

Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

Bread wheat (Triticum aestivum) is a globally important crop, accounting for 20 per cent of the calories consumed by humans. Major efforts are underway worldwide to increase wheat production by extending genetic diversity and analysing key traits, and genomic resources can accelerate progress. But so far the very large size and polyploid complexity of the bread wheat genome have been substantial barriers to genome analysis. Here we report the sequencing of its large, 17-gigabase-pair, hexaploid genome using 454 pyrosequencing, and comparison of this with the sequences of diploid ancestral and progenitor genomes. We identified between 94,000 and 96,000 genes, and assigned two-thirds to the three component genomes (A, B and D) of hexaploid wheat. High-resolution synteny maps identified many small disruptions to conserved gene order. We show that the hexaploid genome is highly dynamic, with significant loss of gene family members on polyploidization and domestication, and an abundance of gene fragments. Several classes of genes involved in energy harvesting, metabolism and growth are among expanded gene families that could be associated with crop productivity. Our analyses, coupled with the identification of extensive genetic variation, provide a resource for accelerating gene discovery and improving this major crop.

/pdf/analysis-of-the-bread-wheat-genome-using-whole-genome-49qkdk9tij.pdf

Analysis of the bread wheat genome using whole-genome shotgun sequencing

Polyploidization has provided much genetic variation for plant adaptive evolution, but the mechanisms by which the molecular evolution of polyploid genomes establishes genetic architecture underlying species differentiation are unclear Brassica is an ideal model to increase knowledge of polyploid evolution Here we describe a draft genome sequence of Brassica oleracea, comparing it with that of its sister species B rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of transposable elements, differential gene co-retention for specific pathways and variation in gene expression, including alternative splicing, among a large number of paralogous and orthologous genes Genes related to the production of anticancer phytochemicals and morphological variations illustrate consequences of genome duplication and gene divergence, imparting biochemical and morphological variation to B oleracea This study provides insights into Brassica genome evolution and will underpin research into the many important crops in this genus

/pdf/the-brassica-oleracea-genome-reveals-the-asymmetrical-2y7hgd5bni.pdf

The Brassica oleracea genome reveals the asymmetrical evolution of polyploid 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

Brassica rapa is one of the most economically important vegetable crops worldwide. Owing to its agronomic importance and phylogenetic position, B. rapa provides a crucial reference to understand polyploidy-related crop genome evolution. The high degree of sequence identity and remarkably conserved genome structure between Arabidopsis and Brassica genomes enables comparative tiling sequencing using Arabidopsis sequences as references to select the counterpart regions in B. rapa, which is a strong challenge of structural and comparative crop genomics. We assembled 65.8 megabase-pairs of non-redundant euchromatic sequence of B. rapa and compared this sequence to the Arabidopsis genome to investigate chromosomal relationships, macrosynteny blocks, and microsynteny within blocks. The triplicated B. rapa genome contains only approximately twice the number of genes as in Arabidopsis because of genome shrinkage. Genome comparisons suggest that B. rapa has a distinct organization of ancestral genome blocks as a result of recent whole genome triplication followed by a unique diploidization process. A lack of the most recent whole genome duplication (3R) event in the B. rapa genome, atypical of other Brassica genomes, may account for the emergence of B. rapa from the Brassica progenitor around 8 million years ago. This work demonstrates the potential of using comparative tiling sequencing for genome analysis of crop species. Based on a comparative analysis of the B. rapa sequences and the Arabidopsis genome, it appears that polyploidy and chromosomal diploidization are ongoing processes that collectively stabilize the B. rapa genome and facilitate its evolution.

/pdf/genome-wide-comparative-analysis-of-the-brassica-rapa-gene-105befyld0.pdf

Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication

Anthocyanins are a major class of flavonoids that are produced in the tissues of many plant species in response to environmental signals. The pigmentation of Chinese cabbage (Brassica rapa) was analyzed using newly developed 300K Brassica rapa microarrays. The significantly expressed genes were analyzed by clusters of orthologous groups (COGs) and hypergeometric analyses for transcription factors associated with anthocyanin pigmentation. The candidate genes were classified into 11 groups that exhibited functionally diverse transcription factor activity involved in anthocyanin-based pigmentation. Thirty-eight unknown genes were identified that potentially play a role in anthocyanin biosynthesis. Three of these unknown genes differed dramatically among cabbage leaves with yellow, green, or red pigmentation. These three genes may play a regulatory role in the anthocyanin production process or may be related to anthocyanin metabolism during flavonoid biosynthesis. These results show functional diversity of transcription factor families and that the biological functions of the anthocyanin-related transcription factors may be activated in a pigmentation signaling pathway in Chinese cabbage (Brassica rapa).

Genetic analysis of gene expression for pigmentation in Chinese cabbage (Brassica rapa)

Therefore, 3,895 candidate genes related to anthocyanin biosynthesis in Chinese cabbage were identified using a 300K Brassica rapa microarray analysis. Gene expression during six stages of leaf developmental stages were examined in FC (green leaf) and FA(red leaf) Chinese cabbage cultivars. The 317 transcription factor genes found to be associated with anthocyanin were classified into 11 functional groups. The ratio of expression levels of each transcription factor between the two cultivars was examined during the six leaf developmental stages. A total of 14 genes were found to be expressed in all developmental stages commonly. Among these genes, 10 unknown and hypothetical genes were differentially revealed to be expressed between the two cultivars at each developmental stage, as determined by microarray analysis, and were verified by RT-PCR validation. These genes most likely play regulatory roles in either anthocyanin production or metabolism during flavonoid biosynthesis. While these genes require further validation and characterization, our results illustrate the potential usefulness of this multi-layered screening method using Chinese cabbage (Brassica rapa) microarrays.

JangHo Hahn

Papers

Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication

Genetic analysis of gene expression for pigmentation in Chinese cabbage (Brassica rapa)

Computational identification of Chinese cabbage anthocyaninspecific genes