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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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Coverage of published Chiifu reference gene models compared with re-annotated Chiifu gene models. Coverage of published Chiifu reference gene models based on number of genes and exons compared with those re-annotated by MAKER, considering a prediction identical when overlapping the reference gene model by at least 75%.
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Fig3: Coverage of published Chiifu reference gene models compared with re-annotated Chiifu gene models. Coverage of published Chiifu reference gene models based on number of genes and exons compared with those re-annotated by MAKER, considering a prediction identical when overlapping the reference gene model by at least 75%.

Mentions: To get a comparable genome annotation for all three B. rapa species, we first re-annotated the Chiifu reference genome using MAKER [14]. This re-annotation covered about 85% of the original 41,019 gene models found in the Brassica database (version 1.2), resulting in 41,052 gene models of which 11,715 were novel predictions (Table 1) [15]. The re-annotation covered about 90% of the exons from the Brassica database (Figure 3). The remaining 6,437 exons, roughly 10%, were mainly (5,615) located in low complexity regions of the genome. As expected, when we decreased the minimum overlap required for matching gene models, the number of recovered gene models increased: only five genes with short lengths (<200 bp) were still missing if the minimum overlap required was 10%. Approximately 75% of re-annotated gene models could be assigned a Gene Ontology term [16].Table 1


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)

Coverage of published Chiifu reference gene models compared with re-annotated Chiifu gene models. Coverage of published Chiifu reference gene models based on number of genes and exons compared with those re-annotated by MAKER, considering a prediction identical when overlapping the reference gene model by at least 75%.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig3: Coverage of published Chiifu reference gene models compared with re-annotated Chiifu gene models. Coverage of published Chiifu reference gene models based on number of genes and exons compared with those re-annotated by MAKER, considering a prediction identical when overlapping the reference gene model by at least 75%.
Mentions: To get a comparable genome annotation for all three B. rapa species, we first re-annotated the Chiifu reference genome using MAKER [14]. This re-annotation covered about 85% of the original 41,019 gene models found in the Brassica database (version 1.2), resulting in 41,052 gene models of which 11,715 were novel predictions (Table 1) [15]. The re-annotation covered about 90% of the exons from the Brassica database (Figure 3). The remaining 6,437 exons, roughly 10%, were mainly (5,615) located in low complexity regions of the genome. As expected, when we decreased the minimum overlap required for matching gene models, the number of recovered gene models increased: only five genes with short lengths (<200 bp) were still missing if the minimum overlap required was 10%. Approximately 75% of re-annotated gene models could be assigned a Gene Ontology term [16].Table 1

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