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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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Subgenome composition of dispensable and unique genes in threeB. rapagenotypes. The subgenome composition of dispensable and unique genes in three B. rapa genotypes in terms of (a) number of genes; (b) frequency of gene changes, calculated as number of changed genes divided by the total number of total genes in the subgenome. LF: less fractionated subgenome, with the highest gene densities; MF1: more fractionated subgenome 1, with moderate gene densities; MF2: most fractionated subgenome 2, with lowest gene densities.
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Fig7: Subgenome composition of dispensable and unique genes in threeB. rapagenotypes. The subgenome composition of dispensable and unique genes in three B. rapa genotypes in terms of (a) number of genes; (b) frequency of gene changes, calculated as number of changed genes divided by the total number of total genes in the subgenome. LF: less fractionated subgenome, with the highest gene densities; MF1: more fractionated subgenome 1, with moderate gene densities; MF2: most fractionated subgenome 2, with lowest gene densities.

Mentions: In total, we thus found 3,672 unique genes, found in only one of the three genomes; all remaining non-unique, non-common genes we called dispensable. About 1,443 out of 2,526 unique and dispensable genes in turnip could be annotated with at least one GO term, as was the case for 1,366 out of 2,328 genes in rapid cycling and 1,649 out of 2,866 in Chiifu. Most of these genes were assigned to only ten biological process GO terms, seven of which were common to the three genomes (Table 3 and Additional file 3). Gene models predicted from contigs that could not be mapped against the Chiifu genome were annotated separately. The number of genes thus found with at least one GO term annotation was 918 for the turnip genome and 548 for the rapid cycling genome (Additional file 4). Most unique and dispensable genes mapped to the LF subgenome, the least mapped to the MF1 subgenome. Corrected for total gene count, the proportion of genes affected by changes to their protein coding region is lowest in the LF subgenome (Figure 7).Table 3


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)

Subgenome composition of dispensable and unique genes in threeB. rapagenotypes. The subgenome composition of dispensable and unique genes in three B. rapa genotypes in terms of (a) number of genes; (b) frequency of gene changes, calculated as number of changed genes divided by the total number of total genes in the subgenome. LF: less fractionated subgenome, with the highest gene densities; MF1: more fractionated subgenome 1, with moderate gene densities; MF2: most fractionated subgenome 2, with lowest gene densities.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig7: Subgenome composition of dispensable and unique genes in threeB. rapagenotypes. The subgenome composition of dispensable and unique genes in three B. rapa genotypes in terms of (a) number of genes; (b) frequency of gene changes, calculated as number of changed genes divided by the total number of total genes in the subgenome. LF: less fractionated subgenome, with the highest gene densities; MF1: more fractionated subgenome 1, with moderate gene densities; MF2: most fractionated subgenome 2, with lowest gene densities.
Mentions: In total, we thus found 3,672 unique genes, found in only one of the three genomes; all remaining non-unique, non-common genes we called dispensable. About 1,443 out of 2,526 unique and dispensable genes in turnip could be annotated with at least one GO term, as was the case for 1,366 out of 2,328 genes in rapid cycling and 1,649 out of 2,866 in Chiifu. Most of these genes were assigned to only ten biological process GO terms, seven of which were common to the three genomes (Table 3 and Additional file 3). Gene models predicted from contigs that could not be mapped against the Chiifu genome were annotated separately. The number of genes thus found with at least one GO term annotation was 918 for the turnip genome and 548 for the rapid cycling genome (Additional file 4). Most unique and dispensable genes mapped to the LF subgenome, the least mapped to the MF1 subgenome. Corrected for total gene count, the proportion of genes affected by changes to their protein coding region is lowest in the LF subgenome (Figure 7).Table 3

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