Human liver aldehyde dehydrogenase in Chinese and Asiatic Indians: Gene deletion and its possible implications in alcohol metabolism

Two separate human liver aldehyde dehydrogenases exist which show differences in substrate specificity, cation inhibition or activation, and molecular weight. In this paper we report a common absence of enzyme 2 in Chinese which may be taken to indicate a gene deletion coding for this enzyme. The possible implication of this gene deletion among Chinese is discussed.     

A novel homozygous 10 nucleotide deletion in BBS10 causes Bardet–Biedl syndrome in a Pakistani family

Bardet–Biedl Syndrome is a multisystem autosomal recessive disorder characterized by central obesity, polydactyly, hypogonadism, learning difficulties, rod-cone dystrophy and renal dysplasia. Bardet–Biedl Syndrome has a prevalence rate ranging from 1 in 100,000 to 1 in 160,000 births although there are communities where Bardet–Biedl Syndrome is found at a higher frequency due to consanguinity. We report here a Pakistani consanguineous family with two affected sons with typical clinical features of Bardet–Biedl Syndrome, in addition to abnormal liver functioning and bilateral basal ganglia calcification, the latter feature being typical of Fahr's disease. Homozygous regions obtained from SNP array depicted three known genes BBS10, BBS14 and BBS2. Bidirectional sequencing of all coding exons by traditional sequencing of all these three genes showed a homozygous deletion of 10 nucleotides (c.1958_1967del), in BBS10 in both affected brothers. The segregation analysis revealed that the parents, paternal grandfather, maternal grandmother and an unaffected sister were heterozygous for the deletion. Such a large deletion in BBS10 has not been reported previously in any population and is likely to be contributing to the phenotype of Bardet–Biedl Syndrome in this family.     

Strong dominance of functional alleles over gene deletions in both intensely growing and deeply starved yeast cells

Previous studies with diploid yeast have shown that the deletion of one allele at a single locus typically has little impact on fitness under conditions promoting fast growth. Here, we confirm and quantify this finding. The strong dominance of functional over nonfunctional alleles is predicted by the metabolic control theory which assumes that the cell is a system of metabolic fluxes and that the total metabolic rate is equivalent to fitness. To test whether these requirements are critical, we tested dominance under conditions of long‐term starvation when metabolism is low and thus the metabolic activities of proteins are likely inadequate or imbalanced. More fundamentally, the central assumption of the model, that high metabolic rate translates into high fitness, appears implausible. Contrary to these conjectures, we found that the mean rate of survival of starving heterozygotes was affected only slightly more than was the mean rate of growth under good conditions. Under none of the two treatments the central prediction of the model, that fitness of heterozygous strains is higher for the enzymatic proteins than for nonenzymatic ones, was confirmed. Our data add to growing uncertainty whether the metabolic control theory is sufficient to explain the remarkable ubiquity of strong genetic dominance.     

EVOLUTIONARY INTERACTIONS BETWEEN SEXUAL AND ALL-FEMALE TAXA OF CYPRINOTUS (OSTRACODA: CYPRIDIDAE)

Freshwater ostracodes show both an exceptionally high incidence of transitions to unisexuality and, in some cases, an extraordinary level of clonal diversity. There is no understanding of the agents promoting these transitions to thelytoky, although it has been suggested that their frequency may set the stage for sexual taxa to infuse clonal diversity into unisexuals. This study examines the nature and origins of clonal diversity in the unisexual ostracode Cyprinotus incongruens. A combination of allozyme and cytogenetic studies revealed the presence of two diploid clones of this species at three temperate sites and ten clones at one arctic site including three diploids, five triploids, and two tetraploids. The low heterozygosity (0%–20%) of its diploid clones suggests that parthenogenesis has arisen spontaneously in C. incongruens rather than through hybridization, as in vertebrate asexuals. Polyploid clones appear to owe their origin to genome additions from sexual taxa, although subsequent mutational divergence has played a role in further enhancing diversity. Two triploid clones have apparently originated from the incorporation of a haploid genome from the sexually reproducing C. glaucus, as evidenced by their high heterozygosity and possession of alleles otherwise found only in that species. Other polyploid clones have likely arisen as a result of interbreeding between bisexual and unisexual C. incongruens. These results suggest that both the incidence of spontaneous transitions to clonality and the frequency of interbreeding with relatives may be the key processes that govern clonal diversity in unisexual ostracodes.     

Climate,Colonisation and Celibacy: Population Structure in Central European Trichomanes speciosum (Pteridophyta)

The Killarney fern Trichomanes speciosum Willd. (Hymenophyllaceae) is unique in possessing both extensive sexual (sporophyte and gametophyte generations present) and asexual (gametophyte only) ranges. It was first discovered in central Europe in 1993 and is represented in this area only by its perennial, vegetatively propagating gametophyte generation. Genetic variation has been investigated at 35 sites. Allozyme diversity is partitioned primarily between, not within, sites. Although genetic variation exists at a fine scale (lt 5 m) within some populations, the results suggest that clones were not intimately associated in these cases. The majority of sites support unique multilocus phenotypes. Where phenotypes were present at more than one site they tended to recur at the next closest site. However, similar phenotypes link eastern and western Pfälzerwald sites up to c. 70 km apart. This pattern of diversity suggests that colonisation was not solely of a “stepping stone” or “leading edge” type. We suggest that during a climatically favourable period, probably the Atlantic hypsithermal, there may have been an explosive colonisation by long-distance dispersal from refugial areas. This was followed by a short period during which sporophyte production, sexual reproduction and local spread were possible. With climatic change, reduction in the available habitat and the loss of the sporophyte generation, different individual genets became fixed within small, favourable, but scattered, sites. The possibility that some central European sites north of the Alps acted as periglacial refugia cannot be discounted, but would appear less likely than (re-) colonisation from the Atlantic fringe.     

Heterokaryon formation and parasexual recombination between vegetatively incompatible lineages in a population of the chestnut blight fungus, Cryphonectria parasitica

Heterokaryosis was recently reported in the chestnut blight fungus, Cryphonectria parasitica, in which individuals contain nuclei that are isogenic except at the mating-type locus (MAT). MAT heterokaryons were found in several natural populations, including a putatively clonal population in West Salem, Wisconsin, providing an opportunity to address the question of how heterokaryons arise. We represented relationships among RFLP fingerprint haplotypes as networks in which loop formation is considered evidence of recombination. From 1990 to 1995, this population was clonal, as indicated by a simple haplotype network without loops, and the correlation of vegetative compatibility (vc) types and mating types with haplotype lineages. By 1999, we observed loops in the haplotype network involving isolates of two vc types (WS-2 and WS-3). Isolates with haplotypes in the loops were either MAT heterokaryons, carried the opposite mating type from other isolates of the same vc type, and/or had two alleles at two or more codominant SCAR (sequence-characterized amplified region) loci. Segregation of markers and recombination were evident among single-spore isolates from one heterokaryon; these single-spore isolates had novel fingerprint haplotypes, also within the loops. In contrast, vc type WS-1, which comprises 85% of the population, was represented by a simple network with no loops, indicating a clonal lineage varying only by mutation. Almost all isolates of WS-1 had the same mating type; the exceptions were five isolates that were MAT heterokaryons. These results are consistent with the hypothesis that heterokaryons formed between vegetatively incompatible individuals, and recombination occurred by a parasexual process.     

Growth,phenology, and biomass allocation of alien Solidago species in central Europe

Plant invasion is a major threat to the integrity of an ecosystem. Exceptionally successful invaders in Europe are the American species of Solidago genus. In this study we examined growth, reproduction, and phenology of Solidago species, of American origin, growing in central Europe (S. altissima, S. canadensis, S. gigantea, S. graminifolia). These taxa were compared with two native species: Solidago virgaurea and Tanacetum vulgare. We observed high differentiation in height, number of shoots, and biomass production between individuals within taxa. Generally, the invasive species produced substantially (two to five times) more biomass than the native ones, being statistically significant in the comparison of alien Solidago graminifolia and S. gigantea versus native S. virgaurea and T. vulgare. The ratio of biomass of reproductive parts to overall biomass varied considerably among years, but generally the lowest one was for Solidago altissima, and the highest for S. graminifolia. It shows a lack of a clear pattern of differentiation between alien and native species in terms of biomass investment in reproduction. We observed a general tendency of allocation of a major part of biomass in rhizomes by phalanx species (S. graminifolia and S. gigantea), while species with guerrilla strategy (S. altissima and S. canadensis) invested more biomass in stems and leaves. However, because of the high variability there was no clear, stable pattern of statistically significant differences between these two groups. The results suggest that S. graminifolia reveals a strong potential of invasion, in spite of its, so far limited, distribution in Europe.     

Development of genome-wide insertion and deletion markers for maize,based on next-generation sequencing data

Background

Insertions and deletions (indels) are the most abundant form of structural variation in all genomes. Indels have been increasingly recognized as an important source of molecular markers due to high-density occurrence, cost-effectiveness, and ease of genotyping. Coupled with developments in bioinformatics, next-generation sequencing (NGS) platforms enable the discovery of millions of indel polymorphisms by comparing the whole genome sequences of individuals within a species.

Results

A total of 1,973,746 unique indels were identified in 345 maize genomes, with an overall density of 958.79 indels/Mbp, and an average allele number of 2.76, ranging from 2 to 107. There were 264,214 indels with polymorphism information content (PIC) values greater than or equal to 0.5, accounting for 13.39 % of overall indels. Of these highly polymorphic indels, we designed primer pairs for 83,481 and 29,403 indels with major allele differences (i.e. the size difference between the most and second most frequent alleles) greater than or equal to 3 and 8 bp, respectively, based on the differing resolution capabilities of gel electrophoresis. The accuracy of our indel markers was experimentally validated, and among 100 indel markers, average accuracy was approximately 90 %. In addition, we also validated the polymorphism of the indel markers. Of 100 highly polymorphic indel markers, all had polymorphisms with average PIC values of 0.54.

Conclusions

The maize genome is rich in indel polymorphisms. Intriguingly, the level of polymorphism in genic regions of the maize genome was higher than that in intergenic regions. The polymorphic indel markers developed from this study may enhance the efficiency of genetic research and marker-assisted breeding in maize.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1797-5) contains supplementary material, which is available to authorized users.