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- Schoch, Conrad L., et al.
(författare)
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Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
- 2014
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Ingår i: Database: The Journal of Biological Databases and Curation. - : Oxford University Press (OUP). - 1758-0463. ; 2014:bau061, s. 1-21
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Tidskriftsartikel (refereegranskat)abstract
- DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
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| 2. |
- Luo, Q.
(författare)
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Optical characteristics of graptolite-bearing sediments and its implication for thermal maturity assessment
- 2018
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Ingår i: International Journal of Coal Geology. - Amsterdam : Elsevier. - 0166-5162 .- 1872-7840. ; 195, s. 386-401
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Tidskriftsartikel (refereegranskat)abstract
- Graptolite reflectance was thought to be one of the most useful thermal maturity indicators for graptolite bearing sediments, however, the relationship between graptolite reflectance and vitrinite reflectance is not well established. Graptolites, especially in the Wufeng–Longmaxi Formations from the Ordovician to Silurian of South China, have been mistaken for vitrinite-like particles or solid bitumen, which results in inconsistent data on the thermal maturity. In this paper, we have employed optical microscope techniques to describe the detailed optical characteristics of graptolites and solid bitumen in the Wufeng–Longmaxi Formations. Laboratory simulation of maturation was used to determine the relationship between graptolite reflectance and vitrinite reflectance. The organic constituents in the Wufeng–Longmaxi Formations are mainly composed of graptolites and solid bitumen. Granular and non-granular graptolites were observed in the Wufeng–Longmaxi Formations, with nongranular as the most common texture. Solid bitumen can be distinguished from non-granular graptolites by its coarse surface, weaker anisotropy, and lower random reflectance. The combination of non-polarized and polarized light is very helpful to distinguish solid bitumen from graptolite. For comparison, organic material from the early Ordovician Alum Shale Formation of Sweden and Estonia was also studied. The macerals of the Alum shales are mainly composed of lamalginites, mineral-bituminous groundmasses, graptolites, and solid bitumen.The major textures of the graptolites in the Sweden and Estonia sediments are non-granular and granular, respectively.Both non-granular graptolite and vitrinite reflectances display a systematic increase with the increase of heating temperature and time. The granular graptolites in the Estonian sample were gradually changed to nongranular graptolites following laboratory simulated maturation, indicating that granular graptolites can transform into non-granular graptolites with maturation. Solid bitumen in the Wufeng–Longmaxi Formations was derived from the solid residue of kerogen and/or post-oil bitumen. The graptolite random reflectance is a better thermal maturity indicator than graptolite maximum reflectance and is more precise due to the smaller standard deviation. Several equations are proposed to determine the thermal maturity of the graptolite-bearing sediments based on graptolite random reflectance, graptolite maximum reflectance and solid bitumen random reflectance.
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