Arabidopsis lyrata

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Selection at Work in Self-Incompatible Arabidopsis lyrata: Mating Patterns in a Natural Population

Selection at Work in Self-Incompatible Arabidopsis lyrata: Mating Patterns in a Natural Population

Identification and characterization of the self-incompatibility genes in Brassicaceae species now allow typing of self-incompatibility haplotypes in natural populations. In this study we sampled and mapped all 88 individuals in a small population of Arabidopsis lyrata from Iceland. The self-incompatibility haplotypes at the SRK gene were typed for all the plants and some of their progeny and used to investigate the realized mating patterns in the population. The observed frequencies of haplotypes were found to change considerably from the parent generation to the offspring generation around their deterministic equilibria as determined from the known dominance relations among haplotypes. We provide direct evidence that the incompatibility system discriminates against matings among adjacent individuals. Multiple paternity is very common, caus- ing mate availability among progeny of a single mother to be much larger than expected for single paternity.

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Natural Variation in MAM Within and Between Populations of Arabidopsis lyrata Determines Glucosinolate Phenotype

Natural Variation in MAM Within and Between Populations of Arabidopsis lyrata Determines Glucosinolate Phenotype

The genetic variation that underlies the glucosinolate phenotype of Arabidopsis lyrata ssp. petraea was investigated between and within populations. A candidate glucosinolate biosynthetic locus (MAM, con- taining methylthioalkylmalate synthase genes) was mapped in A. lyrata to a location on linkage group 6 corresponding to the homologous location for MAM in A. thaliana. In A. thaliana MAM is responsible for side chain elongation in aliphatic glucosinolates, and the MAM phenotype can be characterized by the ratios of long- to short-chain glucosinolates. A quantitative trait loci (QTL) analysis of glucosinolate ratios in an A. lyrata interpopulation cross found one QTL at MAM. Additional QTL were identified for total indolic glucosinolates and for the ratio of aliphatic to indolic glucosinolates. MAM was then used as the candidate gene for a within-population cosegregation analysis in a natural A. lyrata population from Germany. Extensive variation in microsatellite markers at MAM was found and this variation cosegregated with the same glucosinolate ratios as in the QTL study. The combined results indicate that both between- and within-population genetic variation in the MAM region determines phenotypic variation in glucosi- nolate side chains in A. lyrata.

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Natural variation in tolerance to sub-zero temperatures among populations of Arabidopsis lyrata ssp. petraea

Natural variation in tolerance to sub-zero temperatures among populations of Arabidopsis lyrata ssp. petraea

Seeds of Arabidopsis lyrata ssp. petraea were sourced and collected from geographically separated populations within Ireland, Norway, Sweden and Iceland (Table 1). Seed collections were carried out with under permission from all land owners and complied with institutional, na- tional, or international guidelines and legislation. All seeds were half-sibships from the maternal plants. Seeds of each population were sown in Levington M3 compost within individual plug trays. Populations were randomised within each tray and trays were randomly re-positioned every other day. Plants were watered from the base of the pot when required with reverse osmosis (RO) water. No add- itional nutrients were added to the soil or water. Plants were established in controlled-environment growth cabi- nets (Conviron Controlled Environments Limited, Canada) set to a 12/12 h day/night cycle; 20/15 °C day/ night; 60% humidity, atmospheric CO 2 concentration ~

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Linkage Disequilibrium Between Incompatibility Locus Region Genes in the Plant Arabidopsis lyrata

Linkage Disequilibrium Between Incompatibility Locus Region Genes in the Plant Arabidopsis lyrata

We have studied diversity in Arabidopsis lyrata of sequences orthologous to the ARK3 gene of A. thaliana. Our main goal was to test for recombination in the S-locus region. In A. thaliana, the single-copy ARK3 gene is closely linked to the non-functional copies of the self-incompatibility loci, and the ortholog in A. lyrata (a self-incompatible species) is in the homologous genome region and is known as Aly8. It is thus of interest to test whether Aly8 sequence diversity is elevated due to close linkage to the highly polymorphic incompatibility locus, as is theoretically predicted. However, Aly8 is not a single-copy gene, and the presence of paralogs could also lead to the appearance of elevated diversity. We established a typing approach based on different lengths of Aly8 PCR products and show that most A. lyrata haplotypes have a single copy, but some have two gene copies, both closely linked to the incompatibility locus, one being a pseudogene. We determined the phase of multiple haplotypes in families of plants from Icelandic and other populations. Different Aly8 sequence types are associated with different SRK alleles, while haplotypes with the same SRK sequences tend to have the same Aly8 sequence. There is evidence of some exchange of sequences between different Aly8 sequences, making it difficult to determine which ones are allelic or to estimate the diversity. However, the homogeneity of the Aly8 sequences of each S-haplotype suggests that recombination between the loci has been very infrequent over the evolutionary history of these populations. Overall, the results suggest that recombination rarely occurs in the interval between the S-loci and Aly8 and that linkage to the S-loci can probably account for the observed high Aly8 diversity.

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Investigating Incipient Speciation in Arabidopsis lyrata from Patterns of Transmission Ratio Distortion

Investigating Incipient Speciation in Arabidopsis lyrata from Patterns of Transmission Ratio Distortion

ABSTRACT Our understanding of the development of intrinsic reproductive isolation is still largely based on theoretical models and thorough empirical studies on a small number of species. Theory suggests that reproductive isolation develops through accumulation of epistatic genic incompatibilities, also known as Bateson–Dobzhansky–Muller (BDM) incompatibilities. We can detect these from marker transmission ratio distortion (TRD) in hybrid progenies of crosses between species or populations, where TRD is expected to result from selection against heterospecific allele combinations in hybrids. TRD may also manifest itself because of intragenomic conflicts or competition between gametes or zygotes. We studied early stage speciation in Arabidopsis lyrata by investigating patterns of TRD across the genome in F 2 progenies of three reciprocal crosses between four natural populations. We found that the degree of

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Natural variation in tolerance to sub-zero temperatures among populations of Arabidopsis lyrata ssp. petraea

Natural variation in tolerance to sub-zero temperatures among populations of Arabidopsis lyrata ssp. petraea

Seeds of Arabidopsis lyrata ssp. petraea were sourced and collected from geographically separated populations within Ireland, Norway, Sweden and Iceland (Table 1). Seed collections were carried out with under permission from all land owners and complied with institutional, na- tional, or international guidelines and legislation. All seeds were half-sibships from the maternal plants. Seeds of each population were sown in Levington M3 compost within individual plug trays. Populations were randomised within each tray and trays were randomly re-positioned every other day. Plants were watered from the base of the pot when required with reverse osmosis (RO) water. No add- itional nutrients were added to the soil or water. Plants were established in controlled-environment growth cabi- nets (Conviron Controlled Environments Limited, Canada) set to a 12/12 h day/night cycle; 20/15 °C day/ night; 60% humidity, atmospheric CO 2 concentration ~

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Diversity and Linkage of Genes in the Self-Incompatibility Gene Family in Arabidopsis lyrata

Diversity and Linkage of Genes in the Self-Incompatibility Gene Family in Arabidopsis lyrata

We report studies of seven members of the S-domain gene family in Arabidopsis lyrata, a member of the Brassicaceae that has a sporophytic self-incompatibility (SI) system. Orthologs for five loci are identifiable in the self-compatible relative A. thaliana. Like the Brassica stigmatic incompatibility protein locus (SRK), some of these genes have kinase domains. We show that several of these genes are unlinked to the putative A. lyrata SRK, Aly13. These genes have much lower nonsynonymous and synonymous polymorphism than Aly13 in the S-domains within natural populations, and differentiation between populations is higher, consistent with balancing selection at the Aly13 locus. One gene (Aly8) is linked to Aly13 and has high diversity. No departures from neutrality were detected for any of the loci. Comparing different loci within A. lyrata, sites corresponding to hypervariable regions in the Brassica S-loci (SLG and SRK) and in comparable regions of Aly13 have greater replacement site divergence than the rest of the S-domain. This suggests that the high polymorphism in these regions of incompatibility loci is due to balancing selection acting on sites within or near these regions, combined with low selective constraints.

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Identification and Characterization of a Polymorphic Receptor Kinase Gene Linked to the Self-Incompatibility Locus of Arabidopsis lyrata

Identification and Characterization of a Polymorphic Receptor Kinase Gene Linked to the Self-Incompatibility Locus of Arabidopsis lyrata

are linked to a site or sites in a gene that is subject to We recently began a search for orthologues of SRK balancing selection (e.g., Strobeck 1983; Vekemans and SLG in Arabidopsis lyrata (also called Cardaminopsis and Slatkin 1994; Nordborg et al. 1996; Takahata petraea, Arabis petraea, or Arabis lyrata). A. lyrata is one and Satta 1998; Schierup et al. 2000) and has been of the closest relatives of A. thaliana, but is self-incompat- documented in mammalian MHC sequence data (e.g., ible. It is a perennial herb with a circumboreal distribu- Hughes and Yeager 1998). tion. The genus Arabidopsis is a member of the tribe In sporophytic self-incompatibility systems, domi- Arabidae (Rollins 1993) and it is much more distantly nance is possible between pairs of alleles in the determi- related to Brassica than is Raphanus, based on ITS and nation of the pollen phenotype. In Brassica, pollen- NADH sequences (Yang et al. 1999a,b).

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The predominantly selfing plant Arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative Arabidopsis lyrata

The predominantly selfing plant Arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative Arabidopsis lyrata

contrast, Dolgin et al. [21] provided support against the hypothesis based on the Tc1 -like TE family in the self- ing nematode Caenorhabditis elegans and its outcrossing relative C. remanei. We note that existing empirical stu- dies that speak to the effect of inbreeding on TE abun- dance are based on few TE families. No pertinent genome-scale analysis of TEs in closely related selfing and outcrossing species has been available until recently. Such a genome-scale analysis has become possible now that the complete genome sequences of two closely related flowering plant species, Arabidopsis thaliana (strain Col-0) and Arabidopsis lyrata (strain MN47), have become available [22,23]. A. thaliana is a self-com- patible, predominantly selfing plant with an outcrossing rate estimated at approximately 1 to 3% [24-26]. It has a compact genome of 125 Mb [22]. In contrast, A. lyrata is a typically outcrossing species with a genome size exceeding 200 Mb, in which selfing is prevented by the self-incompatibility recognition system controlled by the female and male recognition genes [S-receptor kinase (SRK ), and S-locus cysteine-rich protein (SCR), also known as S-locus protein 11 (SP11 ), respectively] at the S-locus [27-30]. Based on the fossil record and the divergence computed from synonymous substitution rates in the family Brassicaceae at the Chalcone synthase loci (1.0 × 10 -8 - 2.0 × 10 -8 substitutions per site per year) and Alcohol dehydrogenase loci (9.9 × 10 -9 - 2.1 × 10 -8 substitutions per site per year), the split between A. thaliana and other Arabidopsis species including A. lyr- ata occurred 3.1 to 8.3 million years ago (Mya, 95% confidence limit, mean 5.1 Mya) and 3.3 to 9.0 Mya (mean 5.4 Mya), respectively [31]. Other estimates such as 4.2 to 10.9 Mya incorporating data across diverse plants [32,33], 8.7 ± 1.0, 17.9 ± 4.8 Mya using mutation accumulation lines [34], and 8 to 17.9 Mya based on fossil evidence [35] have also been reported. For our analysis, the splitting time estimation from Koch et al. [31] (approx. 5 Mya), which has been commonly used, is most appropriate. The reason is that both the substi- tution rate and the estimate of when self-compatibility arose in A. thaliana are based on this splitting time [36]. We note that the age and abundance distribution of TEs relative to these times, and not their absolute values, are most relevant for this study.

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Molecular Cloning and Characterization of a Candidate Plant Growth Related and Time Keeping Constitutive Cell Surface Hydroquinone (NADH) Oxidase (ENOX1) from Arabidopsis lyrata

Molecular Cloning and Characterization of a Candidate Plant Growth Related and Time Keeping Constitutive Cell Surface Hydroquinone (NADH) Oxidase (ENOX1) from Arabidopsis lyrata

ENOX (ECTO-NOX) proteins are proteins of the external surface of the plasma membrane that cat- alyze oxidation of both NADH and hydroquinones as well as carry out protein disulfide-thiol in- terchange. They exhibit both prion-like and time-keeping (clock) properties. The oxidative and interchange activities alternate to generate a regular period of 24 min in length. Here we report the cloning, expression, and characterization of a plant candidate constitutive ENOX (CNOX or ENOX1) protein from Arabidopsis lyrata. The gene encoding the 335 (165) amino acid protein is found in accession XP-002882467. Functional motifs characteristics of ENOX proteins previously identified by site-directed mutagenesis and present in the candidate ENOX1 protein from plants include adenine nucleotide and copper binding motifs along with essential cysteines. However, the drug binding motif (EEMTE) sequence of human ENOX2 is absent. The activities of the recombi- nant protein expressed in E. coli were unaffected by capsaicin, EGCg, and other ENOX2-inhibiting substances. Periodic oxidative activity was exhibited both with NAD(P)H and reduced coenzyme Q as substrate. Bound copper was necessary for activity and activity was inhibited by the ENOX1- specific inhibitor simalikalactone D. Addition of melatonin phased the 24-min period such that the next complete period began 24 min after the melatonin addition as appeared to be characteristic of ENOX1 activities in general. Periodic protein disulfide-thiol interchange activity also was dem- onstrated along with the 2 oxidative plus 3 interchange activity pattern characteristics of the 24- min ENOX1 protein period. Concentrated solutions of the purified plant ENOX1 protein formed insoluble aggregates, devoid of enzymatic activity, resembling amyloid. Activity was restored to

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Complex Genetic Effects on Early Vegetative Development Shape Resource Allocation Differences Between Arabidopsis lyrata Populations

Complex Genetic Effects on Early Vegetative Development Shape Resource Allocation Differences Between Arabidopsis lyrata Populations

Arabidopsis lyrata (L.) O’Kane and Al-Shehbaz, a peren- nial iteroparous relative of A. thaliana, provides an ideal system to study the genome-to-phenotype processes that give rise to variation in resource allocation strategies. Based on our unpublished observations, the perennial habit in A. lyrata is associated with the presence of indeterminate axil- lary vegetative shoots within the rosette, which persist into subsequent growing seasons, and that resource allocation to vegetative vs. reproductive growth differs widely among populations. Vegetative rosette branching is associated with a transition from broad rosettes dominated by large primary- shoot leaves to more compact branched rosettes with smaller leaves. A. lyrata has a wide but highly fragmented distribution across Europe, Asia, and North America, and occurs in environments that range from subarctic and alpine to warm temperate in climate. A. lyrata also exhibits strong patterns of phenotypic variation between populations in flowering time (Riihimäki and Savolainen 2004; Riihimäki et al. 2005) and fitness components (Kuittinen et al. 2008; Leinonen et al. 2009, 2011). The complete genome se- quence of A. lyrata has now been published (Hu et al. 2011) and genetic and chromosomal synteny maps have been developed (Kuittinen et al. 2004; Schranz et al. 2006), greatly facilitating application of the extensive geno- mic resources and functional information available in A. thaliana to A. lyrata.

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R gene variation across Arabidopsis lyrata subspecies : effects of population structure, selection and mating system

R gene variation across Arabidopsis lyrata subspecies : effects of population structure, selection and mating system

Balancing selection predicts the maintenance of higher levels of diversity and heterozygosity at adaptive loci in in- bred lineages than observed at neutral markers [16, 17], as observed at two of nine R-genes in the selfing Capsella rubella [21]. For N. American A. l. lyrata we found that observed heterozygosity at RAD loci, neutral microsatel- lites and the R-genes were significantly explained by vari- ation in population outcrossing rates (Fig. 3; Additional file 1: Figure S1). Outcrossing populations also tended to have a higher number of haplotypes than selfing popula- tions (Table 1). Interestingly, nucleotide diversity was significantly explained by outcrossing rates at RAD loci and RPM1 (Fig. 4a, b), but not WRR4 (Fig. 4c), with high polymorphism maintained in several of the inbred popula- tions (Table 1). This could reflect the postglacial colonisa- tion of this region by multiple lineages with divergent haplotypes independent of the dominant mating system, as suggested previously [28, 29], but may also be consist- ent with balancing selection. Since the Great Lakes region was colonised within the last 10,000 years, recent bottle- necks and gene flow among lineages arising from inde- pendent colonisation events could reduce signatures of selection. Furthermore, a lack of variation in inbred line- ages might reduce the potential to detect differences in polymorphism resulting from selection. We therefore added a broad-scale perspective to identify signatures of selection by comparing A. l. lyrata with geographically distinct European populations.

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Restriction associated DNA genotyping at multiple spatial scales in Arabidopsis lyrata reveals signatures of pathogen mediated selection

Restriction associated DNA genotyping at multiple spatial scales in Arabidopsis lyrata reveals signatures of pathogen mediated selection

In this study, we used RAD-sequencing of A. lyrata samples from the two subspecies to: (1) compare the resolution of broad- and finer-scale patterns of phylo- geographic structure and genetic variation within these subspecies with previous studies using microsatellite loci or single nucleotide polymorphism genotyping based on relatively few genes; (2) identify regions of the genome showing deviations from this neutral structure character- istic of balancing selection; and (3) test the ability of dif- ferent sampling strategies to detect balancing selection using a test panel of RGAs. We focused our analyses on different subsets of samples from the two subspecies to identify genome-wide patterns of polymorphism and di- vergence. Specifically, we tested for: (a) high diversity and heterozygosity in otherwise low diversity genetic backgrounds, using selfing populations of A. l. lyrata from the North American Great Lakes; and (b) reduced population genetic structure and changes in site fre- quency spectra, using different sets of outcrossing popu- lations sharing a recent postglacial demographic history. We also tested the sensitivity of conclusions to filtering strategies, and compared genome scans using both indi- vidual RAD loci and smoothed genomic regions based on sliding window analyses.

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Comparing the Linkage Maps of the Close Relatives Arabidopsis lyrata and A. thaliana

Comparing the Linkage Maps of the Close Relatives Arabidopsis lyrata and A. thaliana

of A. lyrata ssp. petraea. We used the least-squares method of the Joinmap program for map construction. The gross chromosomal differences between the two species were most parsimoniously explained with three fusions, two reciprocal translocations, and one inversion. The total map length was 515 cM, and the distances were 12% larger than those between corresponding markers in the linkage map of A. thaliana. The 72 markers, consisting of microsatellites and gene-based markers, were spaced on average every 8 cM. Transmission ratio distortion was extensive, and most distortions were specific to each reciprocal cross, suggesting cytoplasmic interactions. We estimate locations and most probable genotype frequencies of transmission ratio distorting loci (TRDL) with a Bayesian method and discuss the possible reasons for the observed distortions.

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Centromere Locations and Associated Chromosome Rearrangements in Arabidopsis lyrata and A. thaliana

Centromere Locations and Associated Chromosome Rearrangements in Arabidopsis lyrata and A. thaliana

Because we start from known A. thaliana genes, we cannot map any genes lost in events such as the hypo- thetical loss of a centromere (see Figure 1). This means that we are unlikely to be able to discover the precise centromere locations of the three A. lyrata chromo- somes involved in fusions. However, fusion events are expected to cause loss of a small numbers of genes, since large deletions are deleterious (K hush and R ick 1968). Moreover, there is no evidence in A. thaliana for non- duplicated genome tracts that might correspond to regions that were duplicates in the ancestral genome, but recently became single copy (B lanc et al. 2003). Thus the fusions often may have been between chro- mosomes with centromeres close to their ends. This implies either that the chromosomes in the ancestor in which the fusions occurred were telocentric or acrocen- tric or that inversions occurred before or during the fusion events to create this situation (see Figure 1). Because no A. lyrata or C. rubella chromosomes are telo- centric (A li et al. 2005), the occurrence of inversions seems likely.

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The structure, organization and radiation of Sadhu non-long terminal repeat retroelements in Arabidopsis species

The structure, organization and radiation of Sadhu non-long terminal repeat retroelements in Arabidopsis species

Low copy number and high divergence among ele- ment subfamilies is not a phenomenon unique to Sadhu elements. Indeed, because only 10% of the Arabidopsis genome is composed of transposable elements [25], lower than other sequenced plant genomes, there may be a general tendency for genome size reduction in this species through progressive loss of repetitive DNA. A comparison of the A. thaliana genome with the five times larger Brassica oleracea genome revealed that while most element families were present in both spe- cies, some (for example, CACTA elements) had contrib- uted more than others to the relative expansion of the Brassica genome [21]. As with the different Sadhu sub- families, different SINE non-LTR subfamilies appear to be more active in each of the two species [26]. The lack of orthologous Sadhu insertion sites among different Arabidopsis species is also reminiscent of the case with SINEs, which similarly featured no shared sites in Table 5 Sadhu elements >350 base pairs (bp) in the Arabidopsis lyrata genome.

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Cytotoxic and antimicrobial activity of selected Cameroonian edible plants

Cytotoxic and antimicrobial activity of selected Cameroonian edible plants

plants consumption, cancer prevention, antimicrobial effects, and overall protection of human health [2]. In Cameroon, medicinal plants consumption is an integral part of dietary behavior, but relatively little is known about their antimicrobial potential and anti-cancer ef- fects. The three selected edible plants studied herein, namely Garcinia lucida Vesque, Fagara heitzii (Guill and Perr) Engl. and Hymenocardia lyrata Tul are recog- nized for their medicinal virtues and have been reported to possess various biological activities. The barks, seeds and leaves of G. lucida are used to treat gastric infec- tions, gynecological infections, diarrheas and as anti- poison [3,4]. It has been reported to have antileishmanial and anti-trypanosomal properties [5,6]. Seeds and barks of Fagara heitzii (Guill and Perr) Engl have been used to treat abdominal pains, asthma, appendicitis and toothache [7]. H. lyrata is well known in Cameroon, where roots and barks are used as antiparasitic, against gastric ulcer and in

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Ecological Succession and Stochastic Variation in the Assembly of Arabidopsis thaliana Phyllosphere Communities

Ecological Succession and Stochastic Variation in the Assembly of Arabidopsis thaliana Phyllosphere Communities

ABSTRACT Bacteria living on the aerial parts of plants (the phyllosphere) are globally abundant and ecologically significant com- munities and can have significant effects on their plant hosts. Despite their importance, little is known about the ecological pro- cesses that drive phyllosphere dynamics. Here, we describe the development of phyllosphere bacterial communities over time on the model plant Arabidopsis thaliana in a controlled greenhouse environment. We used a large number of replicate plants to identify repeatable dynamics in phyllosphere community assembly and reconstructed assembly history by measuring the com- position of the airborne community immigrating to plant leaves. We used more than 260,000 sequences from the v5v6 hyper- variable region of the 16S rRNA gene to characterize bacterial community structure on 32 plant and 21 air samples over 73 days. We observed strong, reproducible successional dynamics: phyllosphere communities initially mirrored airborne communities and subsequently converged to a distinct community composition. While the presence or absence of particular taxa in the phyl- losphere was conserved across replicates, suggesting strong selection for community composition, the relative abundance of these taxa was highly variable and related to the spatial association of individual plants. Our results suggest that stochastic events in early colonization, coupled with dispersal limitation, generated alternate trajectories of bacterial community assembly within the context of deterministic selection for community membership.

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A Vicilin-Like Seed Storage Protein, PAP85, Is Involved in Tobacco Mosaic Virus Replication

A Vicilin-Like Seed Storage Protein, PAP85, Is Involved in Tobacco Mosaic Virus Replication

TMV accumulation was reduced in At3g28770 mutant plants and At3g22640-silenced protoplasts. From the SALK collection (http://signal.salk.edu/), we found individual T-DNA insertion lines corresponding to 9 of the 12 genes. The T-DNA insertion of each SALK line was confirmed by PCR (data not shown). We obtained 8 homozygous mutant lines and 1 heterozygous mutant line (Table 1). We inoculated TMV in the 9 Arabidopsis mutant lines and examined TMV accumulation by RT-PCR 20 days post- FIG 2 Accumulation of TMV inArabidopsis SALK mutant lines and double-stranded RNA (dsRNA)-treated protoplasts. (A) TMV was inoculated inArabidopsis mutant lines. TheArabidopsis mutant lines from the SALK collection were characterized by PCR to confirm their T-DNA insertion (data not shown). Total RNA was extracted from systemic leaves at 20 days postinoculation. TMV CP accumulation was detected by RT-PCR. Ubiquitin 10 was used as a loading control. The lanes 1 to 9 represent SALK_149616C (1), SALK_131250 (2), SALK_136570C (3), SALK_059297C (4), SALK_074253C (5), SALK_020627C (6), SALK_022597 (7), SALK_115514C (8), and SALK_136572C (9) (corresponding to At5g18880, At2g41550, At1g43910, At2g38970, At2g05250, At1g19900, At3g28770, At1g55940, and At5g12100, respectively). Wild-type (WT) Arabidopsis was used as a control. H indicates healthy WT Arabidopsis. (B) qRT-PCR analysis of mRNA levels of At2g34700, At3g22640, and At3g08670 relative to that in mock-inoculated protoplasts (set to 1). Protoplasts were treated with buffer, GFP dsRNA, and gene-specific dsRNA (designed from At2g34700, At3g22640, and At3g08670). Total RNA was extracted at 24 hpi. Data are means ⫾ standard deviations (SD) from 3 experiments. (C) Arabidopsis thaliana protoplasts pretransfected with buffer (buf.) and dsRNA from GFP, At2g34700 (lane 10), At3g22640 (11), and At3g08670 (12). After 24 h, pretreated protoplasts were transfected with TMV, and then cells were collected at 24 hpi. RT-PCR analysis of TMV CP levels in cells was performed with ubiquitin 10 as an internal control. H indicates nontransfected WT Arabidopsis protoplasts.

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The Middle Miocene freshwater mollusk fauna of Lake Gacko (SE Bosnia and Herzegovina): taxonomic revision and paleoenvironmental analysis

The Middle Miocene freshwater mollusk fauna of Lake Gacko (SE Bosnia and Herzegovina): taxonomic revision and paleoenvironmental analysis

lyrata, Prososthenia neutra, Bania valvatoides, Gyrau- lus pulici, Fossarulus moniliferus and Mytilopsis jadro- vi). This is the only occurrence of the dreissenid bi- valve Mytilopsis jadrovi. The unity of both samples is confirmed in the analysis by 83.6 % average similarity. Reduced dissimilarity between clusters 3 and 4 (36.8 %) is rooted in similar abundance values for Fos- sarulus moniliferus and Melanopsis lyrata. The main differences concern the presence of Ferrissia illyrica in Cluster 3 and higher percentage value of Bania valva- toides in Cluster 4. Interestingly, the dissimilarity levels between clusters 1 and 4 (51.0 %) and 2 and 4 (42.0 %), respectively, is lower than that between clus- ters 1 and 3 (66.6 %) and 2 and 3 (53.8 %). In both cases, this can be explained by the recurrence espe- cially of Gyraulus pulici and Bania valvatoides in Clus- ter 4. The major dissimilarity is based on values for Melanopsis lyrata and Prososthenia neutra, which are less common or absent in clusters 1 and 2.

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