Genome-wide SNP discovery and QTL mapping for fruit quality traits in inbred backcross lines (IBLs) of solanum pimpinellifolium using genotyping by sequencing

Çelik, İbrahim; Gürbüz, Nergiz; Uncu, Ali Tevfik; Frary, Anne; Doğanlar, Sami

doi:10.1186/s12864-016-3406-7

Cited by 377 publications

(378 citation statements)

References 41 publications

(82 reference statements)

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“…Microbiota diversity index and composition in the jejunal and ileal digesta were measured in a pooled sample of digesta from six birds per pen (the content of 2 cm jejunum sections per sample) on day 21. To isolate DNA, samples were mixed in a 1:1 ratio with phosphate buffered saline and centrifuged for 5 min at 4°C at 300 × g. Supernatant was collected and centrifuged for 10 min at 4°C at 9000 × g. DNA was extracted from the most sensitive pellet using the QIAamp DNA stool minikit according to the manufacturers' instructions (Schokker et al 2017). Quality and quantity of DNA was checked using the NANOdrop method (Agilent Technologies).…”

Section: Microbiotamentioning

confidence: 99%

Effect of nutritional interventions with quercetin, oat hulls, β-glucans, lysozyme and fish oil on performance and health status related parameters of broilers chickens

Torki

Schokker

Duijster-Lensing³

et al. 2018

British Poultry Science

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1. An experiment was conducted to evaluate the effects of technical feed ingredients between 14 and 28 d of age on performance and health status of broilers (d 14-35) fed diets with a high inclusion rate of rapeseed meal as a nutritional challenge. It was hypothesized that the feed ingredients would improve health status related parameters. 2. A total of 1008 one-day-old male Ross 308 chicks were distributed over 36 floor pens and allocated to one of six iso-caloric (AME 13 MJ/kg) growing diets (d 15-28): a control and five test diets supplemented with quercetin (400 mg/kg), oat hulls (50 g/kg), β-glucan (100 mg/kg), lysozyme (40 mg/kg) or fish oil ω-3 fatty acids (40 g/kg), with six replicate pens per treatment. 3. Dietary inclusion of oat hulls and lysozyme resulted in a reduction in broiler performance during the first week after providing the experimental diets. 4. No effect of interventions on the microbiota diversity in the jejunum and ileum was observed. Ileal microbiota composition of birds fed oat hulls differed from the other groups, as shown by a higher abundance of the genus Enterococcus, mainly at the expense of the genus Lactobacillus. 5. In the jejunum, villus height and crypt depth of lysozyme-fed birds at d 28 were decreased compared to the control group. Higher total surface area of villi occupied by goblet cells and total villi surface area in jejunum (d 21 and 28) were observed in chickens fed oat hulls compared to other groups. 6. Genes related to the growth-factor-activity pathway were more highly expressed in birds fed β-glucan compared to the control group, while the genes related to anion-transmembrane-transporter-activity pathway in the quercetin- and oat hull-fed birds were less expressed. The genes differently expressed between dietary interventions did not seem to be directly involved in immune related processes. 7. It was concluded that the tested nutritional interventions in the current experiment only marginally effected health status related parameters.

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Section: Microbiotamentioning

confidence: 99%

Effect of nutritional interventions with quercetin, oat hulls, β-glucans, lysozyme and fish oil on performance and health status related parameters of broilers chickens

Torki

Schokker

Duijster-Lensing³

et al. 2018

British Poultry Science

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“…The cfDNA sequencing-based method relies on high quality and comprehensive database, but existing genome references of Echinococcus spp. are limited, and only several genome references are available [44,65,66] whose quality is far from perfect. More importantly, sequence contamination is a serious problem for cell-free Echinococcus spp.…”

Section: Plos Neglected Tropical Diseasesmentioning

confidence: 99%

“…Since the Echinococcus spp. tapeworm samples are always separated from host tissue [44,65,66], it is not easy to remove the contamination of host thoroughly by experimental processing. In the process of genome constructing, some host sequences may mix into the parasite sequence, which is a common problem for genomes construction [67].…”

Section: Plos Neglected Tropical Diseasesmentioning

confidence: 99%

Comprehensive characterization of plasma cell-free Echinococcus spp. DNA in echinococcosis patients using ultra-high-throughput sequencing

et al. 2020

PLoS Negl Trop Dis

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Background Echinococcosis is a life-threatening parasitic disease caused by Echinococcus spp. tapeworms with over one million people affected globally at any time. The Echinococcus spp. tapeworms in the human body release DNA to the circulatory system, which can be a biomarker for echinococcosis. Cell-free DNA (cfDNA) is widely used in medical research and has been applied in various clinical settings. As for echinococcosis, several PCR-based tests had been trialed to detect cell-free Echinococcus spp. DNA in plasma or serum, but the sensitivity was about 20% to 25%. Low sensitivity of PCR-based methods might be related to our limited understanding of the features of cell-free Echinococcus spp. DNA in plasma, including its concentration, fragment pattern and release source. In this study, we applied ultra-high-throughput sequencing to comprehensively investigate the characteristics of cell-free Echinococcus spp. DNA in plasma of echinococcosis patients. Methodology/Principal findings We collected plasma samples from 23 echinococcosis patients. Total plasma cfDNA was extracted and sequenced with a high-throughput sequencing platform. An average of 282 million read pairs were obtained for each plasma sample. Sequencing data were analyzed PLOS NEGLECTED TROPICAL DISEASES

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“…Expression of ProQ, a protein that regulates osmolarity via interactions with the ProP transporter, significantly affects sRNA abundance in Salmonella , and has been shown to aid in translation inhibition both by increasing sRNA stability and by blocking ribosome binding on target mRNAs (61, 62). Moreover, potential coevolutionary considerations are not limited to sRNA-binding proteins: a recent comparison of Listeria genomes identified 12 sRNAs that appear to have coevolved with protein-coding genes linked to virulence (63). Further study is needed in order to better understand these coevolutionary dynamics, but their import is becoming increasingly clear.…”

Section: Gain Of Function and Functional Divergencementioning

confidence: 99%

Origin, Evolution, and Loss of Bacterial Small RNAs

Dutcher

Raghavan

2018

Microbiol Spectr

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Despite the central role of bacterial non-coding small RNAs (sRNAs) in posttranscriptional regulation, little is understood about their evolution. Here, we compile what has been studied to date and trace a life cycle of sRNAs—from their mechanisms of emergence, through processes of change and frequent neofunctionalization, to their loss from bacterial lineages. Because they possess relatively unrestrictive structural requirements, we find that sRNA origins are varied, and include de novo emergence as well as formation from pre-existing genetic elements via duplication events and horizontal gene transfer. The need for only partial complementarity to their mRNA targets facilitates apparent rapid change, which also contributes to significant challenges in tracing sRNAs across broad evolutionary distances. We document that recently-emerged sRNAs in particular evolve quickly, mirroring dynamics observed in microRNAs, their functional analogs in eukaryotes. Mutations in mRNA-binding regions, transcriptional regulator or sigma factor binding sites, and protein-binding regions are all likely sources of shifting regulatory roles of sRNAs. Finally, using examples from the few evolutionary studies available, we examine cases of sRNA loss, and describe how these may be the result of adaptive in addition to neutral processes. We highlight the need for more comprehensive analyses of sRNA evolutionary patterns as a means to improve novel sRNA detection, enhance genome annotation, and deepen our understanding of regulatory networks in bacteria.

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Genome-wide SNP discovery and QTL mapping for fruit quality traits in inbred backcross lines (IBLs) of solanum pimpinellifolium using genotyping by sequencing

Cited by 377 publications

References 41 publications

Effect of nutritional interventions with quercetin, oat hulls, β-glucans, lysozyme and fish oil on performance and health status related parameters of broilers chickens

Effect of nutritional interventions with quercetin, oat hulls, β-glucans, lysozyme and fish oil on performance and health status related parameters of broilers chickens

Comprehensive characterization of plasma cell-free Echinococcus spp. DNA in echinococcosis patients using ultra-high-throughput sequencing

Origin, Evolution, and Loss of Bacterial Small RNAs

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