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Beyond genomic variation--comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage.

Lin K, Zhang N, Severing EI, Nijveen H, Cheng F, Visser RG, Wang X, de Ridder D, Bonnema G - BMC Genomics (2014)

Bottom Line: The number of genes with protein-coding changes between the three genotypes was lower than that among different accessions of Arabidopsis thaliana, which can be explained by the smaller effective population size of B. rapa due to its domestication.By analysing genes unique to turnip we found evidence for copy number differences in peroxidases, pointing to a role for the phenylpropanoid biosynthesis pathway in the generation of morphological variation.Our study thus provides two new B. rapa reference genomes, delivers a set of computer tools to analyse the resulting pan-genome and uses these to shed light on genetic drivers behind the rich morphological variation found in B. rapa.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Plant Breeding, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands. guusje.bonnema@wur.nl.

ABSTRACT

Background: Brassica rapa is an economically important crop species. During its long breeding history, a large number of morphotypes have been generated, including leafy vegetables such as Chinese cabbage and pakchoi, turnip tuber crops and oil crops.

Results: To investigate the genetic variation underlying this morphological variation, we re-sequenced, assembled and annotated the genomes of two B. rapa subspecies, turnip crops (turnip) and a rapid cycling. We then analysed the two resulting genomes together with the Chinese cabbage Chiifu reference genome to obtain an impression of the B. rapa pan-genome. The number of genes with protein-coding changes between the three genotypes was lower than that among different accessions of Arabidopsis thaliana, which can be explained by the smaller effective population size of B. rapa due to its domestication. Based on orthology to a number of non-brassica species, we estimated the date of divergence among the three B. rapa morphotypes at approximately 250,000 YA, far predating Brassica domestication (5,000-10,000 YA).

Conclusions: By analysing genes unique to turnip we found evidence for copy number differences in peroxidases, pointing to a role for the phenylpropanoid biosynthesis pathway in the generation of morphological variation. The estimated date of divergence among three B. rapa morphotypes implies that prior to domestication there was already considerably divergence among B. rapa genotypes. Our study thus provides two new B. rapa reference genomes, delivers a set of computer tools to analyse the resulting pan-genome and uses these to shed light on genetic drivers behind the rich morphological variation found in B. rapa.

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Workflow of the study. The workflow describes the methods and logic used in the study, from raw sequence reads to the annotation of the full complement of genes in a genome. Newly created scripts are marked by “Script”. Any number of genomes can be analyzed using this workflow, provided there is sufficient computational power.
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Fig9: Workflow of the study. The workflow describes the methods and logic used in the study, from raw sequence reads to the annotation of the full complement of genes in a genome. Newly created scripts are marked by “Script”. Any number of genomes can be analyzed using this workflow, provided there is sufficient computational power.

Mentions: The two newly-assembled genomes representing the turnip morphotype (turnip) and the oil crop morphotype (rapid cycling), their annotation files, a gene list for the three categories of pan genomes and the Blast2GO project files generated in the study are all provided (Additional files 6, 7, 8 and 9). The genomes can also be browsed at http://www.bioinformatics.nl/brassica/turnip and http://www.bioinformatics.nl/brassica/rapid-cycling. All used software tools in this project can be handled by biologists with some basic bioinformatics skills and the pre-/post-processing scripts are available for download (Table 7, Figure 9 and Additional file 10). These programs were run on an OpenSuSE Linux server with 16 AMD Opteron Processor cores and 128 GB of memory.Table 7


Beyond genomic variation--comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage.

Lin K, Zhang N, Severing EI, Nijveen H, Cheng F, Visser RG, Wang X, de Ridder D, Bonnema G - BMC Genomics (2014)

Workflow of the study. The workflow describes the methods and logic used in the study, from raw sequence reads to the annotation of the full complement of genes in a genome. Newly created scripts are marked by “Script”. Any number of genomes can be analyzed using this workflow, provided there is sufficient computational power.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4230417&req=5

Fig9: Workflow of the study. The workflow describes the methods and logic used in the study, from raw sequence reads to the annotation of the full complement of genes in a genome. Newly created scripts are marked by “Script”. Any number of genomes can be analyzed using this workflow, provided there is sufficient computational power.
Mentions: The two newly-assembled genomes representing the turnip morphotype (turnip) and the oil crop morphotype (rapid cycling), their annotation files, a gene list for the three categories of pan genomes and the Blast2GO project files generated in the study are all provided (Additional files 6, 7, 8 and 9). The genomes can also be browsed at http://www.bioinformatics.nl/brassica/turnip and http://www.bioinformatics.nl/brassica/rapid-cycling. All used software tools in this project can be handled by biologists with some basic bioinformatics skills and the pre-/post-processing scripts are available for download (Table 7, Figure 9 and Additional file 10). These programs were run on an OpenSuSE Linux server with 16 AMD Opteron Processor cores and 128 GB of memory.Table 7

Bottom Line: The number of genes with protein-coding changes between the three genotypes was lower than that among different accessions of Arabidopsis thaliana, which can be explained by the smaller effective population size of B. rapa due to its domestication.By analysing genes unique to turnip we found evidence for copy number differences in peroxidases, pointing to a role for the phenylpropanoid biosynthesis pathway in the generation of morphological variation.Our study thus provides two new B. rapa reference genomes, delivers a set of computer tools to analyse the resulting pan-genome and uses these to shed light on genetic drivers behind the rich morphological variation found in B. rapa.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Plant Breeding, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands. guusje.bonnema@wur.nl.

ABSTRACT

Background: Brassica rapa is an economically important crop species. During its long breeding history, a large number of morphotypes have been generated, including leafy vegetables such as Chinese cabbage and pakchoi, turnip tuber crops and oil crops.

Results: To investigate the genetic variation underlying this morphological variation, we re-sequenced, assembled and annotated the genomes of two B. rapa subspecies, turnip crops (turnip) and a rapid cycling. We then analysed the two resulting genomes together with the Chinese cabbage Chiifu reference genome to obtain an impression of the B. rapa pan-genome. The number of genes with protein-coding changes between the three genotypes was lower than that among different accessions of Arabidopsis thaliana, which can be explained by the smaller effective population size of B. rapa due to its domestication. Based on orthology to a number of non-brassica species, we estimated the date of divergence among the three B. rapa morphotypes at approximately 250,000 YA, far predating Brassica domestication (5,000-10,000 YA).

Conclusions: By analysing genes unique to turnip we found evidence for copy number differences in peroxidases, pointing to a role for the phenylpropanoid biosynthesis pathway in the generation of morphological variation. The estimated date of divergence among three B. rapa morphotypes implies that prior to domestication there was already considerably divergence among B. rapa genotypes. Our study thus provides two new B. rapa reference genomes, delivers a set of computer tools to analyse the resulting pan-genome and uses these to shed light on genetic drivers behind the rich morphological variation found in B. rapa.

Show MeSH