Limits...
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.

Show MeSH

Related in: MedlinePlus

Definition of retained and lost genes. Illustrative examples of a retained and a lost gene in turnip. (a)A. thaliana gene A has three orthologous genes in turnip, but only two in Chiifu and rapid cycling; hence, we call A a retained gene for turnip based on the presence of A3. (b) Gene A is considered a lost gene for turnip based on the absence of A3.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4230417&req=5

Fig2: Definition of retained and lost genes. Illustrative examples of a retained and a lost gene in turnip. (a)A. thaliana gene A has three orthologous genes in turnip, but only two in Chiifu and rapid cycling; hence, we call A a retained gene for turnip based on the presence of A3. (b) Gene A is considered a lost gene for turnip based on the absence of A3.

Mentions: These two new genomes were combined with the reference Chiifu genome (representative of the heading leafy type) to form an initial B. rapa pan-genome. This concept was raised first in the study of bacterial species, to define the full complement of genes of several closely related strains [12]. In a pan-genome, we can distinguish common genes, present in all accessions of a species; dispensable genes, occurring in more than one genome; and unique genes, specific to a single genome [13]. In the B. rapa pan-genome, we find such genes and explore functional annotations of the unique gene set to find morphotype-specific genes. We also analyze the orthology of genes in the pan-genome to Arabidopsis thaliana and Thellungiella halophila to find lost genes (orthologs missing in one of the three B. rapa genomes) and retained genes (orthologs present in only one of the genomes) (FigureĀ 2). Finally, using orthologous genes we estimate the divergence date of the three B. rapa species and find that it far precedes domestication. The two newly assembled and annotated genomes are available to the community as an online resource at http://www.bioinformatics.nl/brassica/turnip and http://www.bioinformatics.nl/brassica/rapid-cycling, accompanied by the tools developed to explore the pan-genome.Figure 2


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)

Definition of retained and lost genes. Illustrative examples of a retained and a lost gene in turnip. (a)A. thaliana gene A has three orthologous genes in turnip, but only two in Chiifu and rapid cycling; hence, we call A a retained gene for turnip based on the presence of A3. (b) Gene A is considered a lost gene for turnip based on the absence of A3.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig2: Definition of retained and lost genes. Illustrative examples of a retained and a lost gene in turnip. (a)A. thaliana gene A has three orthologous genes in turnip, but only two in Chiifu and rapid cycling; hence, we call A a retained gene for turnip based on the presence of A3. (b) Gene A is considered a lost gene for turnip based on the absence of A3.
Mentions: These two new genomes were combined with the reference Chiifu genome (representative of the heading leafy type) to form an initial B. rapa pan-genome. This concept was raised first in the study of bacterial species, to define the full complement of genes of several closely related strains [12]. In a pan-genome, we can distinguish common genes, present in all accessions of a species; dispensable genes, occurring in more than one genome; and unique genes, specific to a single genome [13]. In the B. rapa pan-genome, we find such genes and explore functional annotations of the unique gene set to find morphotype-specific genes. We also analyze the orthology of genes in the pan-genome to Arabidopsis thaliana and Thellungiella halophila to find lost genes (orthologs missing in one of the three B. rapa genomes) and retained genes (orthologs present in only one of the genomes) (FigureĀ 2). Finally, using orthologous genes we estimate the divergence date of the three B. rapa species and find that it far precedes domestication. The two newly assembled and annotated genomes are available to the community as an online resource at http://www.bioinformatics.nl/brassica/turnip and http://www.bioinformatics.nl/brassica/rapid-cycling, accompanied by the tools developed to explore the pan-genome.Figure 2

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
Related in: MedlinePlus