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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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Number of genes predicted to be functionally affected by genomic variants. Before annotation, genes were considered functionally affected in the rapid cycling line or in turnip when one of the following variants was found w.r.t. the Chiifu genome: SPLICE_SITE_ACCEPTOR, SPLICE_SITE_DONOR, START_LOST, EXON_DELETED, FRAME_SHIFT, STOP_GAINED or STOP_LOST. Genes were considered affected if they had no orthologous gene at the same chromosome/scaffold of Chiifu genome after its re-annotation.
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Fig5: Number of genes predicted to be functionally affected by genomic variants. Before annotation, genes were considered functionally affected in the rapid cycling line or in turnip when one of the following variants was found w.r.t. the Chiifu genome: SPLICE_SITE_ACCEPTOR, SPLICE_SITE_DONOR, START_LOST, EXON_DELETED, FRAME_SHIFT, STOP_GAINED or STOP_LOST. Genes were considered affected if they had no orthologous gene at the same chromosome/scaffold of Chiifu genome after its re-annotation.

Mentions: The genome sequences of turnip and rapid cycling were reconstructed by applying all genomic variation found to the reference genome. The total lengths of both resulting genomes were almost the same as that of the reference genome (283.84 Mbs): 282.93 Mbs for turnip and 282.69 Mbs for rapid cycling. Before re-annotation of the reference genomes, nearly half of its gene models appeared to be affected by changes in the protein coding region in either turnip (17,052) or rapid cycling (18,734) with moderate to high impact [17] (Additional file 1). Re-annotation of the turnip and rapid cycling genomes resulted in 40,708 and 40,506 predicted gene models respectively, slightly below the number found in the reference genome (41,052). After re-annotation, the number of genes found in the turnip and rapid cycling genomes which changed function or became pseudogenes with respect to the Chiifu genome was only 2,472 resp. 2,270 (FigureĀ 5).Figure 5


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)

Number of genes predicted to be functionally affected by genomic variants. Before annotation, genes were considered functionally affected in the rapid cycling line or in turnip when one of the following variants was found w.r.t. the Chiifu genome: SPLICE_SITE_ACCEPTOR, SPLICE_SITE_DONOR, START_LOST, EXON_DELETED, FRAME_SHIFT, STOP_GAINED or STOP_LOST. Genes were considered affected if they had no orthologous gene at the same chromosome/scaffold of Chiifu genome after its re-annotation.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig5: Number of genes predicted to be functionally affected by genomic variants. Before annotation, genes were considered functionally affected in the rapid cycling line or in turnip when one of the following variants was found w.r.t. the Chiifu genome: SPLICE_SITE_ACCEPTOR, SPLICE_SITE_DONOR, START_LOST, EXON_DELETED, FRAME_SHIFT, STOP_GAINED or STOP_LOST. Genes were considered affected if they had no orthologous gene at the same chromosome/scaffold of Chiifu genome after its re-annotation.
Mentions: The genome sequences of turnip and rapid cycling were reconstructed by applying all genomic variation found to the reference genome. The total lengths of both resulting genomes were almost the same as that of the reference genome (283.84 Mbs): 282.93 Mbs for turnip and 282.69 Mbs for rapid cycling. Before re-annotation of the reference genomes, nearly half of its gene models appeared to be affected by changes in the protein coding region in either turnip (17,052) or rapid cycling (18,734) with moderate to high impact [17] (Additional file 1). Re-annotation of the turnip and rapid cycling genomes resulted in 40,708 and 40,506 predicted gene models respectively, slightly below the number found in the reference genome (41,052). After re-annotation, the number of genes found in the turnip and rapid cycling genomes which changed function or became pseudogenes with respect to the Chiifu genome was only 2,472 resp. 2,270 (FigureĀ 5).Figure 5

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