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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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Genomic variations anchored to chromosomes in resequenced turnip and rapid cycling genomes. Genomic variants including insertions, deletions and SNPs between resequenced turnip, rapid cycling and reference Chiifu genome on each chromosome. On each chromosome (A01-A10), the middle row represents either common or unique variations in the Chiifue genome. Genomic variations between rapid cycling and Chiifu are presented in the top three rows, variations between turnip and Chiifu in the bottom three rows. Common variations have the same sequence composition at the same position in both rapid cycling and turnip; unique variations have different nucleotides between the three genomes at the same position.
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Fig4: Genomic variations anchored to chromosomes in resequenced turnip and rapid cycling genomes. Genomic variants including insertions, deletions and SNPs between resequenced turnip, rapid cycling and reference Chiifu genome on each chromosome. On each chromosome (A01-A10), the middle row represents either common or unique variations in the Chiifue genome. Genomic variations between rapid cycling and Chiifu are presented in the top three rows, variations between turnip and Chiifu in the bottom three rows. Common variations have the same sequence composition at the same position in both rapid cycling and turnip; unique variations have different nucleotides between the three genomes at the same position.

Mentions: Within a species, the genomic variation between subspecies can vary substantially, as shown in several published intra-species comparative genomic studies [6, 8, 10]. We mapped the turnip and rapid cycling resequenced genomes to the reference Chiifu genome and identified 1,137,171 and 1,308,697 genomic variants respectively (Figure 4). This is less variation than between pairs of A. thaliana accessions [12]. There are 596,323 genomic variations common relative to the reference Chiifu genome (turnip and rapid cycling share the same allele at those sites), 539,747 genomic variations only found between turnip and Chiifu and 711,273 genomic variations only found between rapid cycling and Chiifu. Only 1,101 genomic variations (458,377 bps) are unique, i.e. differ between all three (re) sequenced genomes.Figure 4


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)

Genomic variations anchored to chromosomes in resequenced turnip and rapid cycling genomes. Genomic variants including insertions, deletions and SNPs between resequenced turnip, rapid cycling and reference Chiifu genome on each chromosome. On each chromosome (A01-A10), the middle row represents either common or unique variations in the Chiifue genome. Genomic variations between rapid cycling and Chiifu are presented in the top three rows, variations between turnip and Chiifu in the bottom three rows. Common variations have the same sequence composition at the same position in both rapid cycling and turnip; unique variations have different nucleotides between the three genomes at the same position.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: Genomic variations anchored to chromosomes in resequenced turnip and rapid cycling genomes. Genomic variants including insertions, deletions and SNPs between resequenced turnip, rapid cycling and reference Chiifu genome on each chromosome. On each chromosome (A01-A10), the middle row represents either common or unique variations in the Chiifue genome. Genomic variations between rapid cycling and Chiifu are presented in the top three rows, variations between turnip and Chiifu in the bottom three rows. Common variations have the same sequence composition at the same position in both rapid cycling and turnip; unique variations have different nucleotides between the three genomes at the same position.
Mentions: Within a species, the genomic variation between subspecies can vary substantially, as shown in several published intra-species comparative genomic studies [6, 8, 10]. We mapped the turnip and rapid cycling resequenced genomes to the reference Chiifu genome and identified 1,137,171 and 1,308,697 genomic variants respectively (Figure 4). This is less variation than between pairs of A. thaliana accessions [12]. There are 596,323 genomic variations common relative to the reference Chiifu genome (turnip and rapid cycling share the same allele at those sites), 539,747 genomic variations only found between turnip and Chiifu and 711,273 genomic variations only found between rapid cycling and Chiifu. Only 1,101 genomic variations (458,377 bps) are unique, i.e. differ between all three (re) sequenced genomes.Figure 4

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