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9 results for “internal transcribed spacer 1 (ITS1)”
Supplementary material 4 from: Rosenblad MA, Martín MP, Tedersoo L, Ryberg M, Larsson E, Wurzbacher C, Abarenkov K, Nilsson RH (2016) Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota). MycoKeys 13: 21-33. https://doi.org/10.3897/mycokeys.13.8579
SRP RNA multiple sequence alignment : Explanation note: Multiple sequence alignment with the SRP RNA sequences of Dumesic et al. (2015; Stereum hirsutum, Heterobasidion irregulare, and Heterobasidion annosum) aligned to our newly generated ITS sequences of Russula and Lactarius.
Supplementary material 3 from: Rosenblad MA, Martín MP, Tedersoo L, Ryberg M, Larsson E, Wurzbacher C, Abarenkov K, Nilsson RH (2016) Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota). MycoKeys 13: 21-33. https://doi.org/10.3897/mycokeys.13.8579
ITS/SRP RNA multiple sequence alignment : Explanation note: Multiple sequence alignment comprising the 63 public ITS1 sequences with SRP RNA found in them, the three newly generated sequences, and the SRP RNA sequences from Dumesic et al. (2015) (Stereum hirsutum, Heterobasidion irregulare, and Heterobasidion annosum).
Supplementary material 2 from: Rosenblad MA, Martín MP, Tedersoo L, Ryberg M, Larsson E, Wurzbacher C, Abarenkov K, Nilsson RH (2016) Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota). MycoKeys 13: 21-33. https://doi.org/10.3897/mycokeys.13.8579
ITS multiple sequence alignment : Explanation note: A multiple sequence alignment in the NEXUS format (Maddison et al. 1997) comprising all 63 matching ITS sequences, plus the three newly generated ones (KU356730, KU356731, and KU356732). The alignment was produced in MAFFT without manual adjustment (Katoh and Standley 2013). The alignment is composed of partial nSSU (bases 1-34 in the alignment), the full ITS1 (bases 35-678), the full 5.8S (bases 679-838), the full ITS2 (bases 839-1395), and partial nLSU (bases 1396-end). The SRP RNA occupies position 203-474 in the alignment. The alignment is provided for overview purposes only; the two-order nature of the taxa (Boletales and Russulales) coupled with the high variability of the ITS region jointly mean that the alignment will not be suited for phylogenetic inference.
Supplementary material 1 from: Rosenblad MA, Martín MP, Tedersoo L, Ryberg M, Larsson E, Wurzbacher C, Abarenkov K, Nilsson RH (2016) Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota). MycoKeys 13: 21-33. https://doi.org/10.3897/mycokeys.13.8579
Output from cmsearch and primers used : Explanation note: A) The output from cmsearch showing all 63 relevant matches to the three ectomycorrhizal lineages. B) Detail of the primers used to re-amplify the specimens.
Figure 3 from: Sutton BD, Steck GJ, Norrbom AL, Rodriguez EJ, Srivastava P, Alvarado NN, Colque F, Landa EY, Sánchez JJL, Quisberth E, Peñaranda EA, Clavijo PAR, Alvarez-Baca JK, Zapata TG, Ponce P (2015) Nuclear ribosomal internal transcribed spacer 1 (ITS1) variation in the Anastrepha fraterculus cryptic species complex (Diptera, Tephritidae) of the Andean region. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 175-191. https://doi.org/10.3897/zookeys.540.6147
Figure 3 - Overall similarity inferred by UPGMA (unweighted pair group method with arithmetic mean) cluster analysis (Sneath and Sokal (1973) of Andean Anastrepha fraterculus ITS1 sequence types (489nt). Distances were computed by the maximum composite likelihood method (Tamura et al. (2004) in number of base substitutions per site with gaps eliminated.
Figure 2 from: Sutton BD, Steck GJ, Norrbom AL, Rodriguez EJ, Srivastava P, Alvarado NN, Colque F, Landa EY, Sánchez JJL, Quisberth E, Peñaranda EA, Clavijo PAR, Alvarez-Baca JK, Zapata TG, Ponce P (2015) Nuclear ribosomal internal transcribed spacer 1 (ITS1) variation in the Anastrepha fraterculus cryptic species complex (Diptera, Tephritidae) of the Andean region. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 175-191. https://doi.org/10.3897/zookeys.540.6147
Figure 2 - ITS1 polymorphic region sequences for Andean Anastrepha fraterculus; hypothetical alignment.
Figure 1 from: Rosenblad MA, Martín MP, Tedersoo L, Ryberg M, Larsson E, Wurzbacher C, Abarenkov K, Nilsson RH (2016) Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota). MycoKeys 13: 21-33. https://doi.org/10.3897/mycokeys.13.8579
Figure 1 - Schematic illustration of the fungal ITS region and neighboring rDNA genes. The subregions ITS1, 5.8S, and ITS2 of the ITS region are indicated along with the SRP RNA in the first part of the ITS1. The absolute positions of the subregions and the SRP RNA are provided in Suppl. material 2.
Figure 1 from: Sutton BD, Steck GJ, Norrbom AL, Rodriguez EJ, Srivastava P, Alvarado NN, Colque F, Landa EY, Sánchez JJL, Quisberth E, Peñaranda EA, Clavijo PAR, Alvarez-Baca JK, Zapata TG, Ponce P (2015) Nuclear ribosomal internal transcribed spacer 1 (ITS1) variation in the Anastrepha fraterculus cryptic species complex (Diptera, Tephritidae) of the Andean region. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 175-191. https://doi.org/10.3897/zookeys.540.6147
Figure 1 - Anastrepha fraterculus collection localities.
Figure 4 from: Sutton BD, Steck GJ, Norrbom AL, Rodriguez EJ, Srivastava P, Alvarado NN, Colque F, Landa EY, Sánchez JJL, Quisberth E, Peñaranda EA, Clavijo PAR, Alvarez-Baca JK, Zapata TG, Ponce P (2015) Nuclear ribosomal internal transcribed spacer 1 (ITS1) variation in the Anastrepha fraterculus cryptic species complex (Diptera, Tephritidae) of the Andean region. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 175-191. https://doi.org/10.3897/zookeys.540.6147
Figure 4 - Geographical distribution of Andean Anastrepha fraterculus ITS1 sequence types.
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