Identifying new sex-linked genes through BAC sequencing in the dioecious plant Silene latifolia

Background

Silene latifolia represents one of the best-studied plant sex chromosome systems. A new approach using RNA-seq data has recently identified hundreds of new sex-linked genes in this species. However, this approach is expected to miss genes that are either not expressed or are expressed at low levels in the tissue(s) used for RNA-seq. Therefore other independent approaches are needed to discover such sex-linked genes.

Results

Here we used 10 well-characterized S. latifolia sex-linked genes and their homologs in Silene vulgaris, a species without sex chromosomes, to screen BAC libraries of both species. We isolated and sequenced 4 Mb of BAC clones of S. latifolia X and Y and S. vulgaris genomic regions, which yielded 59 new sex-linked genes (with S. vulgaris homologs for some of them). We assembled sequences that we believe represent the tip of the Xq arm. These sequences are clearly not pseudoautosomal, so we infer that the S. latifolia X has a single pseudoautosomal region (PAR) on the Xp arm. The estimated mean gene density in X BACs is 2.2 times lower than that in S. vulgaris BACs, agreeing with the genome size difference between these species. Gene density was estimated to be extremely low in the Y BAC clones. We compared our BAC-located genes with the sex-linked genes identified in previous RNA-seq studies, and found that about half of them (those with low expression in flower buds) were not identified as sex-linked in previous RNA-seq studies. We compiled a set of ~70 validated X/Y genes and X-hemizygous genes (without Y copies) from the literature, and used these genes to show that X-hemizygous genes have a higher probability of being undetected by the RNA-seq approach, compared with X/Y genes; we used this to estimate that about 30 % of our BAC-located genes must be X-hemizygous. The estimate is similar when we use BAC-located genes that have S. vulgaris homologs, which excludes genes that were gained by the X chromosome.

Conclusions

Our BAC sequencing identified 59 new sex-linked genes, and our analysis of these BAC-located genes, in combination with RNA-seq data suggests that gene losses from the S. latifolia Y chromosome could be as high as 30 %, higher than previous estimates of 10-20 %.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1698-7) contains supplementary material, which is available to authorized users.     

Preservation of the Y transcriptome in a 10-million-year-old plant sex chromosome system

Classical genetic studies discovered loss of genes from the ancient sex chromosome systems of several animals (genetic degeneration), and complete genome sequencing confirms that the heterogametic sex is hemizygous for most sex-linked genes. Genetic degeneration is thought to result from the absence of recombination between the sex chromosome pair (reviewed by [1]) and is very rapid after sex chromosome-autosome fusions in Drosophila [2-4]. Plant sex chromosome systems allow study of the time course of degeneration, because they evolved from a state wholly without sex chromosomes (rather than after a large genome region fused to a preexisting sex chromosome), and, in several taxa, recombination stopped very recently. However, despite increasing genetic and physical mapping of plant nonrecombining sex-determining regions [5-8], it remains very difficult to discover sex-linked genes, and it is unclear whether Y-linked genes are losing full function. We therefore developed a high-throughput method using RNA-Seq to identify sex linkage in Silene latifolia. Recombination suppression between this plant's XY sex chromosome pair started only about 10 million years ago [9]. Our approach identifies several hundred new sex-linked genes, and we show that this young Y chromosome retains many genes, yet these already have slightly reduced gene expression and are accumulating changes likely to reduce protein functions.     

Psychrooligotrophic fungi from Arctic soils of Franz Joseph Land

Microfungi isolated from soil samples collected in Franz Joseph Land by means of the soil dilution and soil washing methods were screened for their ability to grow at low temperatures. The oligotrophic ability of the psychrotrophic strains was then determined on silica gel. A total of 40 taxa from 21 genera were isolated. Most isolates were species of Acremonium, Geomyces, Mortierella, Phialophora, Phoma, Thelebolus and sterile fungi. Eutypella scoparia, Hyphozyma variabilis and Ovadendron sulphureo-ochraceum are new records as soil and Arctic fungi. Most fungal isolates were psychrotrophic. The few psychrooligotrophs were species of Geomyces, Phoma, Thelebolus and Mortierella. Overall, our results suggest that the major component of an Arctic soil mycoflora should be active in one or more short growing seasons interspersed with periods of prolonged dormancy. Only a minor component, such as the small group of psychrooligotrophic fungi found in this study, may be expected to show continuous slow growth. Accepted: 22 November 1998     

A comparison between the 2N and 4N HCl acid-insoluble ash methods for digestibility trials in horses

The digestibility of horse feeds and rations can be determined using different techniques such as calculations based on the chemical composition, in vivo or in vitro methods. The marker methods overcome difficulties like discomfort for the animals and longer experimental times encountered using the ingesta/egesta method. In field conditions, a natural indigestible marker like acid-insoluble ash (AIA), with no changes in the normal ration, could be a very useful tool for digestibility trials. A group of six standardbred horses was used in a set of seven apparent digestibility trials. The diets were based on a first-cut meadow hay added to three different cereals (barley for trials 1 and 2; oats for trials 3 and 5 and corn for trials 6 and 7), the hay : concentrate ratio being 60 : 40 or 70 : 30 on a dry matter basis. Feedstuffs and faeces were analysed to determine the AIA content, using 2N HCl or 4N HCl technique. No differences about AIA concentration were found between the two methods for means and accuracy in each diet. Digestion coefficients for each diet did not differ with AIA method, even if in some trials interfering factors consistently lowered the overall values. Consequently, the AIA 2N HCl can be considered the easier and cheaper method to state apparent digestibility in field conditions, and a good tool for digestibility trials in horses fed hay-based diets.     

Temperature constraints on foraging behaviour of male Alpine ibex (Capra ibex) in summer

In arctic and alpine environments, warm summer temperatures may force a reduction in foraging time of large herbivores, whose tolerance for heat is lower than for species adapted to warmer weather. We constructed time budgets for marked ibex (Capra ibex) males over two summers to test whether warm temperatures constrained foraging behaviour and forced altitudinal migrations. As daily temperature and solar radiation increased, feeding activity was reduced at midday and evening, but increased in the early morning, probably to anticipate for an expected reduction in foraging later in the day. With increasing temperature and solar radiation, ibex moved to higher elevations where they spent very little time feeding. Changes in forage quality and availability could not explain altitudinal migration. Temperatures above 15–20°C apparently result in heat discomfort in male Alpine ibex. As temperature and solar radiation increased, older and larger ibex spent less time feeding during daylight and showed a steeper decrease in feeding time than younger and smaller ibex. Larger males may be more sensitive to temperature and solar radiation, or may have more flexibility in allocating time to different activities, given their lower relative energetic requirements. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Soil persistence and biodiversity of ericoid mycorrhizal fungi in the absence of the host plant in a Mediterranean ecosystem

The occurrence of suitable mycorrhizal inocula may be an important factor affecting the dynamics of plant communities. We investigated the persistence and diversity of ericoid mycorrhizal fungi in the soil of a mature Quercus ilex forest where ericaceous hosts were absent. Erica arborea was used as a bait plant and results were compared to soil samples from experimental plots where cuttings had allowed reappearance of this ericaceous species. Fungal endophytes were isolated and tested in mycorrhiza resynthesis trials. Sterile mycorrhizal endophytes were assigned to morphotypes whose consistency was confirmed by ITS-RFLP. The ITS region of a representative of each morphotype was sequenced. BLAST searches and Neighbour-Joining analysis indicated taxonomic affinities with different classes within Ascomycota. Our results indicate that ericoid mycorrhizal fungi persist and maintain mycorrhizal ability in habitats lacking the ericaceous host. Their persistence could favour the establishment of E. arborea seedlings in pure Q. ilex forests after disturbance phenomena.     

Degradation of cationic surfactants using Pseudomonas putida A ATCC 12633 immobilized in calcium alginate beads

In this study, the degradation of tetradecyltrimethylammonium bromide (TTAB) by freely suspended and alginate-entrapped cells from the bacteria Pseudomonas putida (P. putida) A ATCC 12633 was investigated in batch cultures. The optimal conditions to prepare beads for achieving a higher TTAB degradation rate were investigated by changing the concentration of sodium alginate, pH, temperature, agitation rate and initial concentration of TTAB. The results show that the optimal embedding conditions of calcium alginate beads are 4 % w/v of sodium alginate content and 2 × 10⁸ cfu ml^?1 of P. putida A ATCC 12633 cells that had been previously grown in rich medium. The optimal degradation process was carried out in pH 7.4 buffered medium at 30 °C on a rotary shaker at 100 rpm. After 48 h of incubation, the free cells degraded 26 mg l^?1 of TTAB from an initial concentration of 50 mg l^?1 TTAB. When the initial TTAB concentration was increased to 100 mg l^?1, the free cells lost their degrading activity and were no longer viable. In contrast, when the cells were immobilized on alginate, they degraded 75 % of the TTAB after 24 h of incubation from an initial concentration of 330 mg l^?1 of TTAB. The immobilized cells can be stored at 4 °C for 25 days without loss of viability and can be reused without losing degrading capacity for three cycles.     

Active miniature transposons from a plant genome and its nonrecombining Y chromosome

Mechanisms involved in eroding fitness of evolving Y chromosomes have been the focus of much theoretical and empirical work. Evolving Y chromosomes are expected to accumulate transposable elements (TEs), but it is not known whether such accumulation contributes to their genetic degeneration. Among TEs, miniature inverted-repeat transposable elements are nonautonomous DNA transposons, often inserted in introns and untranslated regions of genes. Thus, if they invade Y-linked genes and selection against their insertion is ineffective, they could contribute to genetic degeneration of evolving Y chromosomes. Here, we examine the population dynamics of active MITEs in the young Y chromosomes of the plant Silene latifolia and compare their distribution with those in recombining genomic regions. To isolate active MITEs, we developed a straightforward approach on the basis of the assumption that recent transposon insertions or excisions create singleton or low-frequency size polymorphisms that can be detected in alleles from natural populations. Transposon display was then used to infer the distribution of MITE insertion frequencies. The overall frequency spectrum showed an excess of singleton and low-frequency insertions, which suggests that these elements are readily removed from recombining chromosomes. In contrast, insertions on the Y chromosomes were present at high frequencies. Their potential contribution to Y degeneration is discussed.