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- Groenen, M. A., et al.
(författare)
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Analyses of pig genomes provide insight into porcine demography and evolution
- 2012
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 491:7424, s. 393-398
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Tidskriftsartikel (refereegranskat)abstract
- For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars approximately 1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.
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| 2. |
- Jayasiri, Subashini C., et al.
(författare)
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The Faces of Fungi database: fungal names linked with morphology, phylogeny and human impacts
- 2015
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Ingår i: Fungal diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 74:1, s. 3-18
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Tidskriftsartikel (refereegranskat)abstract
- Taxonomic names are key links between various databases that store information on different organisms. Several global fungal nomenclural and taxonomic databases (notably Index Fungorum, Species Fungorum and MycoBank) can be sourced to find taxonomic details about fungi, while DNA sequence data can be sourced from NCBI, EBI and UNITE databases. Although the sequence data may be linked to a name, the quality of the metadata is variable and generally there is no corresponding link to images, descriptions or herbarium material. There is generally no way to establish the accuracy of the names in these genomic databases, other than whether the submission is from a reputable source. To tackle this problem, a new database (FacesofFungi), accessible at www.facesoffungi.org (FoF) has been established. This fungal database allows deposition of taxonomic data, phenotypic details and other useful data, which will enhance our current taxonomic understanding and ultimately enable mycologists to gain better and updated insights into the current fungal classification system. In addition, the database will also allow access to comprehensive metadata including descriptions of voucher and type specimens. This database is user-friendly, providing links and easy access between taxonomic ranks, with the classification system based primarily on molecular data (from the literature and via updated web-based phylogenetic trees), and to a lesser extent on morphological data when molecular data are unavailable. In FoF species are not only linked to the closest phylogenetic representatives, but also relevant data is provided, wherever available, on various applied aspects, such as ecological, industrial, quarantine and chemical uses. The data include the three main fungal groups (Ascomycota, Basidiomycota, Basal fungi) and fungus-like organisms. The FoF webpage is an output funded by the Mushroom Research Foundation which is an NGO with seven directors with mycological expertise. The webpage has 76 curators, and with the help of these specialists, FoF will provide an updated natural classification of the fungi, with illustrated accounts of species linked to molecular data. The present paper introduces the FoF database to the scientific community and briefly reviews some of the problems associated with classification and identification of the main fungal groups. The structure and use of the database is then explained. We would like to invite all mycologists to contribute to these web pages.
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| 3. |
- Soares, Pedro R., et al.
(författare)
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Drought effects on soil organic carbon under different agricultural systems
- 2023
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Ingår i: Environmental Research Communications (ERC). - : IOP Publishing. - 2515-7620. ; 5:11
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Forskningsöversikt (refereegranskat)abstract
- Drought is a natural hazard occurring with increasing frequency due to climate change. Drought events reduce soil water content and also soil organic carbon (SOC) content, with negative impacts on crop development and food security. This study investigates the impact of drought on SOC dynamics in agricultural systems and the influence of water availability and farm management practices in these impacts. The manuscript is a systematic review, based on Scopus database for scoping the literature on the topic. A total of 283 records were retrieved, but only 16 papers were relevant for the review. The main findings are: (1) water plays a key role in regulating SOC mineralization due to its impact on dynamics of soil microbial communities, necessitating further research on water management to mitigate carbon losses during drought; (2) different agricultural systems can have differing impacts on SOC under drought conditions depending on crop type (e.g. pastures are more resilient than arable systems) and farm management practices; and (3) SOC loss generally occurs after a drought event, regardless of farm management regime, but the contribution of drought to this loss requires further research. Best management practices, such as cover cropping and soil amendment, can minimize SOC losses, but further research is required to optimize these practices in counteracting the effect of drought. A better understanding of the effects of drought on SOC dynamics, and of short-term and long-term ways to mitigate these effects, is important to ensure soil health and crop productivity.
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| 4. |
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| 5. |
- Zeng, Z. K., et al.
(författare)
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A new Buttiauxella phytase continuously hydrolyzes phytate and improves amino acid digestibility and mineral balance in growing pigs fed phosphorous-deficient diet
- 2016
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Ingår i: Journal of Animal Science. - : Oxford University Press (OUP). - 0021-8812 .- 1525-3163. ; 94:2, s. 629-638
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Tidskriftsartikel (refereegranskat)abstract
- Ten ileal T-cannulated pigs (19.26 ± 1.06 kg) were used to evaluate the effects of a novel Buttiauxella phytase on apparent ileal digestibility (AID) of AA and apparent total tract digestibility (ATTD) and hindgut disappearance of DM, GE, CP, crude fiber, NDF, and ADF as well as minerals balance. Pigs were fed in a duplicated 5 × 4 incomplete Latin square design (5 diets with 4 periods). Each period consisted of a 5-d adjustment period followed by a 3-d total collection of feces and urine and then a 2-d collection of ileal digesta. The 5 diets included a P-deficient basal diet (0.43% Ca and 0.38% total P) that was supplemented with 0 (negative control [NC]), 500, 1,000, or 20,000 phytase units (FTU)/kg phytase and a positive control (PC) diet that was P adequate (0.64% Ca and 0.52% total P). The addition of phytase to the NC diet improved (P < 0.05) AID of phytate from 11.1 to 62.8, 70.6, and 90.5% at the inclusion rates of 500, 1,000, and 20,000 FTU/kg, respectively. In general, phytase supplementation at a dose of 20,000 FTU/kg further increased (P < 0.05) AID of Ca, total P, and phytate and reduced (P < 0.05) the ileal phytate concentration compared with diets with 500 or 1,000 FTU/kg phytase. Pigs fed the diet with 20,000 FTU/kg phytase but not diets with 500 and 1,000 FTU/kg phytase showed improved (P < 0.05) ATTD of CP and AID of DM, GE, CP, Leu, Lys, Thr, Val, Asp, and Ser compared with pigs fed the PC or NC diet. However, hindgut disappearance of crude fiber and NDF (P < 0.05) were reduced in pigs fed the diet with 20,000 FTU/kg phytase compared with pigs fed the PC or NC diet. Pigs fed diets with 500 or 1,000 FTU/ kg phytase had greater ATTD and retention of Ca and P than pigs fed the NC diet but less compared with pigs fed the diet with 20,000 FTU/kg phytase. Supplementation of 20,000 FTU/kg phytase to the NC diet improved (P < 0.05) digestibility of Na, Mn, and Zn as well as retention (%) of Zn. Increasing phytase supplementation doses from 0 to 1,000 FTU/kg linearly improved (P < 0.05) retention of Mg; meanwhile, digestibility of Mg and Mn and AID of Thr showed a linear increase trend (P = 0.084). In conclusion, supplementation of the novel Buttiauxella phytase at doses up to 20,000 FTU/kg hydrolyzed most of the phytate (90%) and consequently further improved mineral and protein utilization.
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