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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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Network analysis of retained and lost genes in turnip. 155 A. thaliana peroxidase-related genes were selected. a) Five retained genes and four lost genes were identified in turnip, five of which were class III peroxidases. b) Summary of the functional protein interaction network found by STRING using five retained genes as input. c) Phenylpropanoid biosynthesis pathway in A. thaliana, including four retained genes and two lost genes. A. thaliana genes that encode enzymes are indicated by light green colored boxes; red resp. dark green boxes indicate genes with less resp. more copies in rapid cycling than in Chiifu and turnip.
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Fig8: Network analysis of retained and lost genes in turnip. 155 A. thaliana peroxidase-related genes were selected. a) Five retained genes and four lost genes were identified in turnip, five of which were class III peroxidases. b) Summary of the functional protein interaction network found by STRING using five retained genes as input. c) Phenylpropanoid biosynthesis pathway in A. thaliana, including four retained genes and two lost genes. A. thaliana genes that encode enzymes are indicated by light green colored boxes; red resp. dark green boxes indicate genes with less resp. more copies in rapid cycling than in Chiifu and turnip.

Mentions: Next, we specifically looked for genes potentially related to morphological variation, by considering retained and lost genes with orthologs in both A. thaliana and T. halophila. Only a small percentage of these, 15% of the retained and 10% of the lost genes, could be categorized into known A. thaliana gene families (Table 6). The set of unique and dispensable genes found in turnip is enriched for the GO cellular component term “peroxisome”, and contains Class III peroxidases among both lost (AT5G64120) and retained (AT1G05260 with gene symbol RCI3) genes. To refine our understanding of a possible role of peroxidases in turnip formation, we more closely investigated B. rapa genes orthologous to 155 peroxidase related genes in A. thaliana[20]. We exploited synteny information to support the confidence in orthology predictions and to help distinguishing true orthologs, since A. thaliana and B. rapa are evolutionary very close [21]. B. rapa orthologs of five A. thaliana genes were retained and of four A. thaliana genes were lost in turnip compared to Chiifu and rapid cycling (Figure 8a). We found proteins functionally interacting with these genes using STRING (Figure 8b) [22]. Four of the five retained genes were involved in the phenylpropanoid biosynthesis pathway and the fifth, AT3G63080 (ATGPX5), a glutathione peroxidase, may contribute to glutathione synthesis. Only one of the four A. thaliana orthologs of the lost genes, AT5G64120 (PER71), was predicted to interact with other proteins in STRING, whereas both PER71 and another lost gene AT1G77100 (PER13) are also involved in phenylpropanoid biosynthesis. We then examined all genes known to be involved in the phenylpropanoid biosynthesis pathway in A. thaliana and found that while orthologs of genes encoding a peroxidase (EC number 1.11.1.7) were enriched in turnip, genes encoding a 4-coumarate-CoA ligase (EC 6.2.1.12) or a coniferyl-alcohol glucosyltransferase (EC 2.4.1.111) were underrepresented. The six A. thaliana genes encoding this ligase have ten orthologs in the common gene set of B. rapa, but only two B. rapa genes are orthologous to three A. thaliana genes coding for the glucosyltransferase. This suggests the lower copy number of genes in turnip coding for the glucosyltransferase may cause the reduction of 4-D-glucoside, coniferin, syringin and hence increase the production of different lignins (Figure 8c).Table 6


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)

Network analysis of retained and lost genes in turnip. 155 A. thaliana peroxidase-related genes were selected. a) Five retained genes and four lost genes were identified in turnip, five of which were class III peroxidases. b) Summary of the functional protein interaction network found by STRING using five retained genes as input. c) Phenylpropanoid biosynthesis pathway in A. thaliana, including four retained genes and two lost genes. A. thaliana genes that encode enzymes are indicated by light green colored boxes; red resp. dark green boxes indicate genes with less resp. more copies in rapid cycling than in Chiifu and turnip.
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Related In: Results  -  Collection

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Fig8: Network analysis of retained and lost genes in turnip. 155 A. thaliana peroxidase-related genes were selected. a) Five retained genes and four lost genes were identified in turnip, five of which were class III peroxidases. b) Summary of the functional protein interaction network found by STRING using five retained genes as input. c) Phenylpropanoid biosynthesis pathway in A. thaliana, including four retained genes and two lost genes. A. thaliana genes that encode enzymes are indicated by light green colored boxes; red resp. dark green boxes indicate genes with less resp. more copies in rapid cycling than in Chiifu and turnip.
Mentions: Next, we specifically looked for genes potentially related to morphological variation, by considering retained and lost genes with orthologs in both A. thaliana and T. halophila. Only a small percentage of these, 15% of the retained and 10% of the lost genes, could be categorized into known A. thaliana gene families (Table 6). The set of unique and dispensable genes found in turnip is enriched for the GO cellular component term “peroxisome”, and contains Class III peroxidases among both lost (AT5G64120) and retained (AT1G05260 with gene symbol RCI3) genes. To refine our understanding of a possible role of peroxidases in turnip formation, we more closely investigated B. rapa genes orthologous to 155 peroxidase related genes in A. thaliana[20]. We exploited synteny information to support the confidence in orthology predictions and to help distinguishing true orthologs, since A. thaliana and B. rapa are evolutionary very close [21]. B. rapa orthologs of five A. thaliana genes were retained and of four A. thaliana genes were lost in turnip compared to Chiifu and rapid cycling (Figure 8a). We found proteins functionally interacting with these genes using STRING (Figure 8b) [22]. Four of the five retained genes were involved in the phenylpropanoid biosynthesis pathway and the fifth, AT3G63080 (ATGPX5), a glutathione peroxidase, may contribute to glutathione synthesis. Only one of the four A. thaliana orthologs of the lost genes, AT5G64120 (PER71), was predicted to interact with other proteins in STRING, whereas both PER71 and another lost gene AT1G77100 (PER13) are also involved in phenylpropanoid biosynthesis. We then examined all genes known to be involved in the phenylpropanoid biosynthesis pathway in A. thaliana and found that while orthologs of genes encoding a peroxidase (EC number 1.11.1.7) were enriched in turnip, genes encoding a 4-coumarate-CoA ligase (EC 6.2.1.12) or a coniferyl-alcohol glucosyltransferase (EC 2.4.1.111) were underrepresented. The six A. thaliana genes encoding this ligase have ten orthologs in the common gene set of B. rapa, but only two B. rapa genes are orthologous to three A. thaliana genes coding for the glucosyltransferase. This suggests the lower copy number of genes in turnip coding for the glucosyltransferase may cause the reduction of 4-D-glucoside, coniferin, syringin and hence increase the production of different lignins (Figure 8c).Table 6

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