Evolution of biological interaction networks: from models to real data

We are beginning to uncover common mechanisms leading to the evolution of biological networks. The driving force behind these advances is the increasing availability of comparative data in several species.     

Beyond genomic variation - comparison and functional annotation of three Brassica rapa genomes: a turnip,a rapid cycling and a Chinese cabbage

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.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-250) contains supplementary material, which is available to authorized users.     

Characterization of the MLO gene family in Rosaceae and gene expression analysis in Malus domestica

Background

Powdery mildew (PM) is a major fungal disease of thousands of plant species, including many cultivated Rosaceae. PM pathogenesis is associated with up-regulation of MLO genes during early stages of infection, causing down-regulation of plant defense pathways. Specific members of the MLO gene family act as PM-susceptibility genes, as their loss-of-function mutations grant durable and broad-spectrum resistance.

Results

We carried out a genome-wide characterization of the MLO gene family in apple, peach and strawberry, and we isolated apricot MLO homologs through a PCR-approach. Evolutionary relationships between MLO homologs were studied and syntenic blocks constructed. Homologs that are candidates for being PM susceptibility genes were inferred by phylogenetic relationships with functionally characterized MLO genes and, in apple, by monitoring their expression following inoculation with the PM causal pathogen Podosphaera leucotricha.

Conclusions

Genomic tools available for Rosaceae were exploited in order to characterize the MLO gene family. Candidate MLO susceptibility genes were identified. In follow-up studies it can be investigated whether silencing or a loss-of-function mutations in one or more of these candidate genes leads to PM resistance.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-618) contains supplementary material, which is available to authorized users.     

Molecular and pharmacological characterisation of the MSH-R alleles in Swiss cattle breeds

The coat colour in mammals is determined by the relative amounts of eumelanin (black/brown) and phaeomelanin (red/yellow), produced in melanocytes, which are controlled by melanocyte stimulating hormone receptor (MSH-R). Melanocyte stimulating hormone receptor is activated by alpha-melanocyte-stimulating hormone (alpha-MSH). Stimulated MSH-R activates adenylyl cyclase (AC), thereby increasing the amount of cyclic AMP in the cell, which activates the enzyme tyrosinase resulting in eumelanin synthesis. In this study the complete coding sequences of five alleles of the MSH-R gene found in Holstein, Red Holstein, Simmental, and Brown Swiss cattle were cloned into a mammalian expression vector and transfected into human embryonic kidney (HEK) 293 cells. The expressed receptors were analyzed for their ability to increase intracellular cAMP in response to stimulation by alpha-MSH. The recessive red allele (e) found in Red Holstein and Simmental and the dominant black allele (ED) found in Holstein were unresponsive to a wide range of alpha-MSH concentrations. Two alleles from Brown Swiss (E(d1), E(d2)) and one allele found in the Simmental breed (e(f)) responded to stimulation by alpha-MSH in a dose-dependent manner. When compared to E(d1) and E(d2), the cells transfected with the e(f) MSH-R allele, however, reached the corresponding intracellular cAMP concentrations at a 10-fold higher concentration of alpha-MSH. In conjunction with the mode of inheritance of coat colour, the results indicate that the e MSH-R allele is a non-functional receptor, E(D) is constitutively activated receptor, and E(d1) and E(d2) are hormonally activated receptors. The delay in e(f) MSH-R response may explain the similarity between the e and e(f) phenotypes.     

Progeny testing of heterozygote carriers of the Robertsonian translocation 1/29 in Bovidae

In our recent population study, 220 daughters of a heterozygote carrier of the Robertsonian translocation 1/29 were analysed by screening of metaphase spreads and typing of microsatellite markers. The segregation between markers near the centromere of chromosomes 1 and 29 and the fusion were analysed. The microsatellite markers were selected from the USDA, MARC cattle genome map. Analyses were done on AGLA17, BM6438, TGLA49, BMS 1928, BM8139, INRA117, BMS574, BMS711 and BMS4015 of chromosome 1, and on BM4602, BMC2228 and BMS1857 of chromosome 29. The two markers BMC2228 and BMS4018 in the linkage group originating from the fusion were able to either recognise or exclude 167 daughters out of 220 as carriers of the Robertsonian translocation 1/29. Fifty-three daughters showed double heterozygote markers like their father, and were therefore not informative. The use of conventional cytogenetics in combination with molecular studies has allowed a more precise evaluation of the Robertsonian translocations than either approach alone might have done.     

Chromosome configurations and time sequence of the first meiotic division in bovine oocytes matured in vitro

Bovine oocytes aspirated from small follicles were cultured for various time periods. Subsequently, the oocytes were fixed and stained with Giemsa and analyzed for their chromosome configuration. The appearance of the various chromosome configurations and their time sequence were documented. The influence of the presence or absence of follicle-stimulating hormone (FSH) during culture was studied. No difference was found in the proportion of oocytes completing meiotic maturation in the presence or absence of FSH. On average, 75% of the oocytes reached metaphase II after 20 h. FSH showed two main effects: 1) all the cumulus oocyte complexes incubated longer than 10 h in the presence of FSH showed cumulus expansion, and 2) the time period required for chromosome condensation was prolonged for 3 h in the presence of FSH. However, the time sequence in vitro in the presence as well as in the absence of FSH paralleled the time sequence found in vivo, where variations of several hours have been reported. The delay in chromosome condensation in the presence of FSH was assumed to be due to a transient increase in cyclic adenosine 3',5'-monophosphate in the cumulus oocyte complexes. As demonstrated for FSH, the described culture system allowed the study of individual factors for their influence on meiotic maturation of bovine oocytes.