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152 results for “ITS2”
Figure 3. ITS2 in A Heterolepidoderma and Halichaetoderma gen. nov. (Gastrotricha: Chaetonotidae) riddle: integrative taxonomy and phylogeny of six new freshwater species from Central Europe
Figure 3. ITS2 molecule of the genera Heterolepidoderma and Halichaetoderma gen. nov. A, putative consensus secondary structure. The central loop radiates four helices. However, helix I could not be incorporated into the consensus 2D structure due to its very high variability in length and nucleotide composition (see Figure 2). By contrast, helix II was the most conservative having 9–11 pairs and invariably seven nucleotides in its terminal loop. Helix III was distinctly longer than helix II (32–55 nt vs. 25–31 nt). Although being more variable than helix II, helix III consistently displayed a motif 5'-UUGGG vs. YYYAA-3' at its base. Helix IV was the longest, had 52–112 ribonucleotides, and usually ran along helix II according to the 3D modelling. For localization of helix 10, which is made by the interaction of the 3ʹ-end of 5.8S and the 5ʹ-end of 28S, see Figure 4. B, two different views on the tertiary structure, showing that helices II and IV run in parallel. C, structure logos of helices II‒IV. The height of a base is proportional to its frequency in the multiple sequence alignment.
FIGURE 209. ITS2 gene tree. Collection stop numbers for G in Crickets of the genus Gryllus in the United States (Orthoptera: Gryllidae: Gryllinae)
FIGURE 209. ITS2 gene tree. Collection stop numbers for G. lightfooti samples (orange): S07-61 (G1099, G1206); S07-66 (G1218); S07-67 (G1222); S07-68 (G1133); S09-55 (G1369); S12-19 (G2253); S12-102 (G2404); S12-103 (G2414); S13-13 (G2518, G2528); S13-16 (G2480, G2513, G2519, G2520); S13-18 (G2484, G2696); S13-19 (G2505, G2527, G2533, G2592); S15-49 (G3104); S15-75 (G3061, G3063); S15-100 (G3340); S15-104 (G3328); S15-105 (G3317, G3332); S15-109 (G3333); S15-110 (G3214, G3228, G3235, G3236, G3237); S16-24 (G3435, G3445, G3448, G3450); S16-31 (G3438, G3444); S16- 33 (G3443). Collection stop numbers for G. sotol samples (purple): S15-77 (G3295); S17-4 (G3493, G3497, G3503, G3505, G3508, G3509, G3510, G3511). Collection stop numbers for G. transpecos samples (blue): S07-36 (G1081); S09-64 (G1370, G1384, G1393); S15-61 (G3189, G3279, G3346); S15-64 (G3314, G3348, G3349); S15-65 (G3117, G3138, G3139, G3274, G3327); S15-68 (G3062); S15-69 (G3067); S15-72 (G3059, G3060, G3065, G3069, G3350); S16-2 (G3376, G3377, G3383, G3384, G3389, G3391); S16-3 (G3379, G3385, G3388, G3395); S16-7 (G3375); S16-8 (G3368, G3417); S16-9 (G3396); S16- 10 (G3369); S16-12 (G3398); S16-14 (G3380). Note the two ITS2 clades of G. sotol.
FIGURE 206. ITS2 in Crickets of the genus Gryllus in the United States (Orthoptera: Gryllidae: Gryllinae)
FIGURE 206. ITS2 gene tree, indicating multilocus DNA clade based on locality. G. veletis samples: S03-58 (G39); S03-60 (G30); S15-9 (G2939); S15-16 (G2927, G2934); S15-21 (G2895); S15-24 (G2936); S15-25 (G2968, G2983); S15-53 (G3343); S15-62 (G3131, G3134, G3304); S15-67 (G3137, G3144). G. montis samples: S07-53 (G1046, G1047, G1048); S07-54 (G1123, G1226); S07-58 (G1051, G1094, G1216); S07-59 (G1095, G1096, G1126); S07-60 (G1052, G1097, G1127, G1128, G1201); S07-62 (G1102, G1151); S07-63 (G1129); S07-65 (G1103, G1132); S08-50 (G690, G691); S09-50 (G1353); S12-18 (G2241, G2249); S12-22 (G2273); S12-30 (G2251); S12-103 (G2416); S13-17 (G2472, G2475, G2857); S13-18 (G2461, G2471, G2482; S13-21 (G2462, G2464, G2466, G2467); S13-36 (G2487, G2489, G2491); Parker Canyon Lake, Cochise Co., AZ (2004-44, 45, 50, 73); Madera Canyon, Bog Springs, Santa Cruz Co., AZ (2004-118, 2005-003, 004, 009, 012); Miller Canyon, Huachuca Mts., Cochise Co., AZ (2005-169, 176, 180, 181, 182); Reef Camp, Huachuca Mts., Cochise Co., AZ (2012-219, 220, 222, 223, 226). G. longicercus samples: S12-23 (G2245, G2247, G2260, G2261); S15-52 (G3086, G3276).
FIGURE 224. ITS2 gene tree. Collection stop numbers for G in Crickets of the genus Gryllus in the United States (Orthoptera: Gryllidae: Gryllinae)
FIGURE 224. ITS2 gene tree. Collection stop numbers for G. longicercus samples: S09-64 (G1388, G1395); S11-93 (G2175, G2176); S12-23 (G2245, G2247, G2260, G2261); S15-52 (G3086, G3276); S15-56 (G3160, G3179); S15-63 (G3149, G3223, G3303); S15-77 (G3177); S15-110 (G3213); S16-2 (G3418); S16-4 (G3386, G3390, G3392, G3401, G3453); S17-4 (G3522, G3523, G3528). Collection stop numbers for G. vulcanus samples: S07-46 (G1030, G1032, G1033); S07-52 (G1050, G1146); type locality (2016-025).
FIGURE 157. ITS2 gene tree. G in Crickets of the genus Gryllus in the United States (Orthoptera: Gryllidae: Gryllinae)
FIGURE 157. ITS2 gene tree. G. cohni samples: S95-81 (G102); S14-53, 20 km S Mazatlán, Mexico (G2756, G2757, G2776, G2843, G2844, G2846); S15-107 (G3248); S15-108 (G3217); Cordes Junction, Yavapai Co., AZ (2003-294, 2003-295A); Bloody Basin x Pueblo la Plata, Agua Fria National Monument, Yavapai Co., AZ (2006-248). G. vocalis samples: S05-68 (G487); S05- 99 (G505); S11-102 (G2185); S12-20 (G2244); S12-26 (G2265); S13-13 (G2531); S13-14 (G2479); S13-16 (G2481); S15-110 (G3215); S15-111 (G3219, G3224, G3227, G3290, G3291); S16-18 (G3405); S16-28 (G3423); Wet Beaver Creek Campground, Yavapai Co., AZ (2007-172, 2007-174); California State University Northridge, Los Angeles Co., CA (2016-043). G. alogus, type locality, Albuquerque, NM (G3335, G3337).
FIGURE 191. ITS2 gene tree. Collection stop numbers for G in Crickets of the genus Gryllus in the United States (Orthoptera: Gryllidae: Gryllinae)
FIGURE 191. ITS2 gene tree. Collection stop numbers for G. chisosensis: S07-36 (G1192); S16-13 (G3399, G3400). Collection stop numbers for G. veletisoides: S03-21 (G9, G10); S03-23 (G11); S06-30 (G540, G541, G566); S12-41 (G2252); S15-81 (G3167, G3174, 2016-044).
FIGURE 98. ITS2 gene tree and distribution map for both G. armatus and G in Crickets of the genus Gryllus in the United States (Orthoptera: Gryllidae: Gryllinae)
FIGURE 98. ITS2 gene tree and distribution map for both G. armatus and G. integer showing both geographic separation and zone of possible hybridization. Collection stop numbers for G. armatus: S04-121 (G358, G359); S05-110 (G511, G512, G513, G515); S07-26 (G1165); S07-33 (G1077); S07-79 (G1228); S10-62 (G1918); S10-63 (G1899); S11-90 (G2172); S12- 36 (G2264); S12-104 (G2411); S13-18 (G2473); S13-46 (G2566); S15-54 (G3096, G3077, G3081); S15-71 (G3101, G3074); S15-73 (G3072); Albuquerque, NM (2003-175); Cordes Junction, AZ (2006-241); Agua Fria, AZ (2006-244). Collection stop numbers for G. integer: S03-100 (G58, G59); S04-36 (G243); S04-40 (G210); S0455 (G245, G246); S04-60 (G218); S04-128 (G370); S05-23 (G477); S05-99 (G499); S06-77 (G629); S09-109 (G1439); S09-114 (G1441, G1445); S11-72 (G2113, G2148); S11-73 (G2143); S12-116 (G2431); S15-80 (G3195, G3316); S15-91 (G3178, G3265); S15-95 (G3292); S16-21 (G3416); S17-6 (G3502, G3525); S16-5 (G3374, G3381); S16-12 (G3366); Hwy 276 mile 30 Sinclair Gas, Garfield Co., UT (2003-038, 2003-039, 2003-041); Winslow, AZ (2003-312, 2012-029, 2012-030, 2012-031, 2012-032).
FIGURE 73. ITS2 gene tree. G in Crickets of the genus Gryllus in the United States (Orthoptera: Gryllidae: Gryllinae)
FIGURE 73. ITS2 gene tree. G. rubens samples: Orlando, FL (F122); Lake City & Ocala, FL (Genbank SRA, Berdan et al. 2016); G. regularis samples: S07-2 (G1101); S07-41 (G1085); S15-67 (G3154); S15-102 (G3280); G. texensis samples: S15-43 (G3048); S16-12 (G3382, G3403, G3404, G3421); Uvalde, TX (d102); Bastrop, TX (d1042).
FIGURE 62. ITS2 gene tree. G in Crickets of the genus Gryllus in the United States (Orthoptera: Gryllidae: Gryllinae)
FIGURE 62. ITS2 gene tree. G. assimilis samples: S10-64 (G1901); S16-12 (G3367, G3373); G. multipulsator sample: S03- 41 (G577); G. locorojo sample: type locality (Rainbow Mealworms); G. veintinueve samples: S02-39 (G134); S07-21 (G1139); S07-27 (G1140, G1211); S09-71 (G1451); OK, Love Co., Hwy 32 at Boggy Creek (2015-055).
Fig. 4 Haplotype networks for ITS2 in Cryptic species of Notophyllum (Polychaeta: Phyllodocidae) in Scandinavian waters
Fig. 4 Haplotype networks for ITS2. (A, B) Notophyllum foliosum. (C, D) N. crypticum n. sp. For further explanations, see Figure 3 10 4 5 3 8 9 B T 6 7 2 T 1 B
Figure 2. Proposed general secondary structure model for the ITS1–5.8S rDNA–ITS2 in A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes
Figure 2. Proposed general secondary structure model for the ITS1–5.8S rDNA–ITS2–LSU rDNA of Opalinida* The expansion segments (ES#L) containing helices (in red) where there are important differences between genera are annotated. Colour code: yellow* ITS1 region; blue* 5.8S rRNA; magenta* ITS2 region; grey* LSU rRNA.
Fig. 6 ITS2 in Species delimitation polyphasic approach reveals Meyerella similis sp. nov.: a new species of "small green balls" within the Chlorella-clade (Trebouxiophyceae, Chlorophyta)
Fig. 6 ITS2 secondary structure of strains ACSSI 346, ACSSI 362, and ACSSI 363 and strains of Meyerella planktonica. CBC in ITS2 secondary structure of the studied strains compared to M. planktonica are denoted by black arrows
FIGURE 2. Bayesian phylogram obtained from general ITS2 in Strobilomyces pteroreticulosporus (Boletales), a new species of the S. strobilaceus complex from the Republic of Korea and remarks on the variability of S. confusus
FIGURE 2. Bayesian phylogram obtained from general ITS2 sequence alignment. Porphyrellus porphyrosporus was used as outgroup taxon. Support values in either Bayesian (Posterior Probabilities values, BPP) or maximum likelihood (ML Bootstrap percentage, MLB) analyses are indicated. Only BPP values over 0.70 and MLB values over 50 % are given above clade branches. Newly sequenced collections are in bold.
FIGURE 1. Ribosomal DNA ITS2 in A newly recognized species in the Anopheles Hyrcanus Group and molecular identification of related species from the Republic of South Korea (Diptera: Culicidae)
FIGURE 1. Ribosomal DNA ITS2 sequence for five Anopheles Hyrcanus Group species from the Republic of South Korea. Bases in the gray areas are common to all species. Speciesspecific primers and direction of amplification are indicated by arrows: sin = An. sinensis, unk1 = An. unknown 1, pul = An. pullus, unk2 = An. unknown 2, les = An. lesteri. Two numbers are given at the end of the figure: 1) ITS2 length, and 2) total length of amplified fragment, which includes 135 bases from the flanking regions.
FIGURE 59. ITS2 sequence alignment for putative species sequenced here. Where identical ITS2 in Cardicola Short, 1953 and Braya n. gen. Digenea: Sanguinicolidae) from five families of tropical Indo-Pacific fishes (
FIGURE 59. ITS2 sequence alignment for putative species sequenced here. Where identical ITS2 sequences were obtained from sanguinicolids of different host/location combinations (not differentiated by morphological comparisons) only one representative sequence has been included here. Gaps of five spaces delineate the 5' and 3' ends of ITS2 (and subsequent 3' end of 5.8S and the 5' end of 28S).
FIGURE 1. ITS2 sequence alignment for threadlike sanguinicolids. Where identical ITS2 in An exceptionally rich complex of Sanguinicolidae von Graff, 1907 (Platyhelminthes: Trematoda) from Siganidae, Labridae and Mullidae (Teleostei: Perciformes) from the Indo-west Pacific Region
FIGURE 1. ITS2 sequence alignment for threadlike sanguinicolids. Where identical ITS2 sequences were obtained for sanguinicolids from different host/location combinations only one sequence has been included here. Gaps of five spaces delineate the 5' and 3' ends of ITS2 (and subsequent 3' end of 5.8S and the 5' end of 28S).
FIGURE 1. Ribosomal DNA ITS2 in Molecular confirmation of Anopheles (Anopheles) lesteri from the Republic of South Korea and its genetic identity with An. (Ano.) anthropophagus from China (Diptera: Culicidae)
FIGURE 1. Ribosomal DNA ITS2 sequence for potential malaria vectors belonging to Anopheles (Anopheles) Hyrcanus Group from Korea, China, Japan and the Philippines. See Table 2 and text for sequence summaries and discussion. The following GenBank accession numbers correspond to the label numbers at the 5' end of the sequence: 1) AY375464; 2) AY375465; 3) AJ004942; 4) AY375466; 5) AF384172, AJ004941 and AF543860; 6) AY375467; 7) AY187728; 8) AY375468; 9) AY375469; 10) AY375470; 11) AY375471. The number of individuals sequenced, of those presented here for the first time, appears in parentheses
FIGURE 1. Phylogenetic tree derived from ITS1 and ITS2 in Taxonomic identity of the Iranian diploid Triticum as evidenced by nrDNA ITS analysis
FIGURE 1. Phylogenetic tree derived from ITS1 and ITS2 sequences inferred by the Neighbor-Joining method using the Kimura 2- parameter model; all bootstrap values over 50% are shown. Sequences obtained from the NCBI are marked with the sequence accession numbers. Aegilops tauschii sequence was defined as an outgroup in the analysis. Clades 1 and 2 are associated with Triticum monococcum s. lat. and T. urartu, respectively.
FIGURE 2. Phylogenetic relationships between T. cinnabarinus and T. urticae inferred from ITS2 in Genetic Relationship between the Carmine Spider Mite Tetranychus cinnabarinus (Boisduval) and the Two-spotted Mite T. urticae Koch in China Based on the mtDNA COI and rDNA ITS2 Sequences
FIGURE 2. Phylogenetic relationships between T. cinnabarinus and T. urticae inferred from ITS2 data of Neighbor- Joining methods. Phylogenetic tree was established by MEGA based on Kimura-2-parameter distance. Numbers on branches indicate the percentage of 100 bootstraps supporting the branching pattern shown. Two sequences of T. evansi and T. pacificus were used as outgroups.
FIGURE 1 in Genetic Relationship between the Carmine Spider Mite Tetranychus cinnabarinus (Boisduval) and the Two-spotted Mite T. urticae Koch in China Based on the mtDNA COI and rDNA ITS2 Sequences
FIGURE 1. Phylogenetic tree inferred from COI sequences of various samples of T. urticae and T. cinnabarinus. The Neighbor-Joining (NJ) method was used based on distances calculated using Kimura-2-parameter correction method. Numbers on branches indicate the percentage of 100 bootstraps supporting the branching pattern shown. The species Petrobia harti and Bryobia kissophila were used as outgroups. Mite colouration for each sample is indicated in brackets: (R) means red form of T. urticae; (G) means green form of T. urticae.
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