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Sorbus aucuparia subsp. pohuashanensis

ABSTRACT: Sorbus aucuparia subsp. pohuashanensis Raw sequence reads

PROVIDER: PRJNA386392 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5533436.fastq.gz	Fastqsanger.gz
	SRR5574440.fastq.gz	Fastqsanger.gz
	SRR5574480.fastq.gz	Fastqsanger.gz
	SRR5574441.fastq.gz	Fastqsanger.gz
	SRR5574442.fastq.gz	Fastqsanger.gz

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Genetic Diversity and Structure of Rear Edge Populations of <i>Sorbus aucuparia</i> (Rosaceae) in the Hyrcanian Forest.

Project description:Sorbus aucuparia (Rosaceae) is a small tree species widely distributed in Eurasia. The Hyrcanian forest is the southernmost distribution limit of this species. Severe habitat degradation and inadequate human interventions have endangered the long-term survival of this species in this region, and it is necessary to develop and apply appropriate management methods to prevent the loss of its genetic diversity. In this study, we used 10 SSR markers in order to evaluate the genetic diversity of this taxon. Leaf samples were collected from five known populations of S. aucuparia throughout its distribution area in the Hyrcanian forest. Expected heterozygosity ranged from 0.61 (ASH) to 0.73, and according to the M-ratio, all populations showed a significant reduction in effective population size, indicating a genetic bottleneck. Global FST was not statistically significant and attained the same values with and without excluding null alleles (ENA) correction (FST = 0.12). Bayesian analysis performed with STRUCTURE defined two genetic clusters among the five known populations, while the results of discriminant analysis of principal components (DAPC) identified three distinct groups. The average proportion of migrants was 22. In general, the gene flow was asymmetrical, with the biggest differences between immigration and emigration in Barzekoh and Asbehriseh. The Mantel test showed that there was no significant correlation between genetic distance (FST) and geographic distance in S. aucuparia. The best pathway for theoretical gene flow is located across the coast of the Caspian Sea and significant spatial autocorrelation was observed in only one population. In order to reduce the extinction risk of very small and scattered populations of S. aucuparia in the Hyrcanian forest, it is very important to establish and/or enhance the connectivity through habitat restoration or genetic exchange.

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Data-dependent acquisition based proteomic analysis of Mycobacterium avium subsp. paratuberculosis ATCC 19698

Project description:Detection of species-specific proteotypic peptides for accurate and easy characterization of infectious non-tuberculous mycobacteria such as Mycobacterium avium subsp. paratuberculosis is essential. Therefore, we conducted an in-depth global proteomic experiment using M. avium subsp. paratuberculosis ATCC 19698 (Map) strain followed by proteome database search and spectral library generation. The lysate was subjected to in-solution proteomic sample preparation and fractionated using an offline C18 StageTip. Each fraction was acquired in technical triplicates using a 180 min data-dependent acquisition (DDA) method in Orbitrap Fusion Tribrid (Thermo Scientific) mass spectrometer. The resulting raw DDA data were searched against the M. avium subsp. paratuberculosis proteome database using Proteome Discoverer and FragPipe. The resulting peptide spectrum matches were converted into a spectral library using BiblioSpec.

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Competitive success of southern populations of Betula pendula and Sorbus aucuparia under simulated southern climate experiment in the subarctic.

Project description:Global warming has been commonly accepted to facilitate species' range shifts across latitudes. Cross-latitudinal transplantations support this; many tree species can well adapt to new geographical areas. However, these studies fail to capture species' adaptations to new light environment because the experiments were not designed to explicitly separate species' responses to light and temperature. Here we tested reaction norms of tree seedlings in reciprocal transplantations 1,000 km apart from each other at two latitudes (60°N and 69°N). In contrast to past studies, we exposed our experimental plants to same temperature in both sites (temperature of 60°N growing site is recorded to adjust temperature of 69°N site in real time via Internet connection) while light environment (photoperiod, light quality) remained ambient. Shoot elongation and autumn coloration were studied in seedlings of two deciduous trees (Betula pendula and Sorbus aucuparia), which were expected to respond differently to day length. Sorbus as a member of Rosaceae family was assumed to be indifferent to photoperiod, while Betula responds strongly to day length. We hypothesized that (1) southern and northern populations of both species perform differently; (2) southern populations perform better in both sites; (3) autumn phenology of southern populations may delay in the northern site; (4) and Sorbus aucuparia is less dependent on light environment. According to the hypotheses, shoot elongation of northern population was inherently low in both species. An evolutionary consequence of this may be a competitive success of southern populations under warming climate. Southern population of B. pendula was delayed in autumn coloration, but not in growth cessation. Sorbus aucuparia was less responsive to light environment. The results suggest that light provides selection pressure in range shifts, but the response is species dependent.

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MicroRNA expression profile of bovine monocyte derived macrophages infected with Mycobacterium avium subsp. Paratuberculosis

Project description:In order to gain a better understanding of MAP infection in immature macrophages, high-throughput sequencing technology was used to perform an analysis of miRNAs profiles of bovine monocyte derived macrophages upon MAP infection.The total numbers of raw reads collected from the MAP-infected and control MDM cells were 14.3 and 17.0 million raw reads per library.The length distribution of the clean reads was focused on 21–24 nt in length and read counts of 22 nt were highest.A total of 510 mature miRNAs were identified, among these a total of 433 miRNAs were homologous to bovine, while 77 were predicted as novel miRNAs that not homologous to any species.The analyses of differential expression revealed 21 DE miRNAs in MDM challenged with MAP compared to the control MDM, Among the DE miRNAs, 14 were upregulated and 7 were downregulated.Furthermore, The GO and KEGG pathway enrichment of these miRNA targets were performed.

2019-04-16 | GSE129819 | GEO

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