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274 results for “nuclear sequence”
Figure 8 from: Justi SA, Dale C (2021) Designation of the neotype of Triatoma dimidiata (Latreille, 1811) (Hemiptera, Reduviidae, Triatominae), with full integrated redescription including mitogenome and nuclear ITS-2 sequences. ZooKeys 1076: 9-24. https://doi.org/10.3897/zookeys.1076.72835
Figure 8 Legs of Triatoma dimidiata neotype (male) A detail of the pair of subapical denticles present on the forelegs B pair of subapical denticles present on the midlegs. Hindlegs do not present denticles.
Supplementary material 2 from: Justi SA, Dale C (2021) Designation of the neotype of Triatoma dimidiata (Latreille, 1811) (Hemiptera, Reduviidae, Triatominae), with full integrated redescription including mitogenome and nuclear ITS-2 sequences. ZooKeys 1076: 9-24. https://doi.org/10.3897/zookeys.1076.72835
GenBank numbers list
Figure 3 from: Shi W, Wen J, Zhao Y, Johnson G, Pan B (2017) Reproductive biology and variation of nuclear ribosomal ITS and ETS sequences in the Calligonum mongolicum complex (Polygonaceae). PhytoKeys 76: 71-88. https://doi.org/10.3897/phytokeys.76.10428
Figure 3 - Maximum likelihood tree for 43 (in-group) Calligonum nrITS and ETS sequences produced with RAxML. Numbers adjacent to (relevant) nodes represent maximum likelihood value and Bayesian posterior probabilities. Branches marked with an asterisk collapse on the maximum likelihood strict consensus tree of the same dataset. The branch marked with a number sign collapses on the Bayesian majority rule consensus tree of the same dataset.
Figure 4 from: Shi W, Wen J, Zhao Y, Johnson G, Pan B (2017) Reproductive biology and variation of nuclear ribosomal ITS and ETS sequences in the Calligonum mongolicum complex (Polygonaceae). PhytoKeys 76: 71-88. https://doi.org/10.3897/phytokeys.76.10428
Figure 4 - Neighbour-net analyses of the Calligonum mongolicum complex, Calligonum ebinuricum, Calligonum calliphysa and closely related taxa based on uncorrected p-distances. Numbers indicate bootstrap values over 1000 replicates.
Figure 2 from: Shi W, Wen J, Zhao Y, Johnson G, Pan B (2017) Reproductive biology and variation of nuclear ribosomal ITS and ETS sequences in the Calligonum mongolicum complex (Polygonaceae). PhytoKeys 76: 71-88. https://doi.org/10.3897/phytokeys.76.10428
Figure 2 - Equatorial view of pollen grains of the Calligonum mongolicum complex under SEM micrographs.1 Calligonum mongolicum 2 Calligonum chinense 3 Calligonum gobicum 4 Calligonum pumilum and 5. Calligonum zaidamense.
Figure 1 from: Shi W, Wen J, Zhao Y, Johnson G, Pan B (2017) Reproductive biology and variation of nuclear ribosomal ITS and ETS sequences in the Calligonum mongolicum complex (Polygonaceae). PhytoKeys 76: 71-88. https://doi.org/10.3897/phytokeys.76.10428
Figure 1 - The phenological phases of the Calligonum mongolicum complex. 1 Calligonum mongolicum 2 Calligonum chinense 3 Calligonum gobicum 4 Calligonum pumilum and 5 Calligonum zaidamense.
Figure 5 from: Compton JA, Schrire BD, Könyves K, Forest F, Malakasi P, Mattapha S, Sirichamorn Y (2019) The Callerya Group redefined and Tribe Wisterieae (Fabaceae) emended based on morphology and data from nuclear and chloroplast DNA sequences. PhytoKeys 125: 1-112. https://doi.org/10.3897/phytokeys.125.34877
Figure 5 Wisteriopsisjaponica (Siebold & Zucc.) J.Compton & Schrire. A Habit B stipels C lower surface of leaflet D flower bud with bract and bracteoles E flower F1 calyx outer surface F2 calyx inner surface and detail of hairs G standard petal inner surface H wing petal I keel petal J staminal column K ovary and style L pods M pod interior and seed N ventral view of seed O lateral view of seed A–C, E–K from Maximowicz s.n.. 1863 D from Oldham 386, L–O from Togasi MSM1, 1950. Drawn by Margaret Tebbs.
Plate 1 from: Compton JA, Schrire BD, Könyves K, Forest F, Malakasi P, Mattapha S, Sirichamorn Y (2019) The Callerya Group redefined and Tribe Wisterieae (Fabaceae) emended based on morphology and data from nuclear and chloroplast DNA sequences. PhytoKeys 125: 1-112. https://doi.org/10.3897/phytokeys.125.34877
Plate 1 Endosamara, Sigmoidala and Kanburia. A, BEndosamararacemosa, Thailand, Sakon Nakhon Prov., S.Mattapha s.n.. C, DSigmoidalakityana Thailand, Nan Prov. S.Mattapha 1117EKanburiachlorantha Thailand, Kanchanaburi Prov. Y.Sirichamorn Y2014-15-1FKanburiatenasserimensis Thailand, Ratchaburi, Khao Chon waterfall Y.Sirichamorn YS2015-8.
Plate 3 from: Compton JA, Schrire BD, Könyves K, Forest F, Malakasi P, Mattapha S, Sirichamorn Y (2019) The Callerya Group redefined and Tribe Wisterieae (Fabaceae) emended based on morphology and data from nuclear and chloroplast DNA sequences. PhytoKeys 125: 1-112. https://doi.org/10.3897/phytokeys.125.34877
Plate 3 Wisteriopsis and Wisteria. AWisteriopsisjaponica, Cultivated, J.C.Raulston Arboretum, North Carolina 980008-17 BWisteriopsisjaponica Japan, Honshu near Kyoto G.Lewis, unvouchered C, DWisteriopsisjaponica, Cultivated, J.C.Raulston Arboretum, North Carolina 980008-17 EWisteriopsisreticulata Cultivated, J.Compton s.n.. unvouchered FWisteriafrutescens Cultivated, B.Schrire unvouchered GWisteriabrachybotrys cultivated, B.Schrire unvouchered.
Figure 4 from: Compton JA, Schrire BD, Könyves K, Forest F, Malakasi P, Mattapha S, Sirichamorn Y (2019) The Callerya Group redefined and Tribe Wisterieae (Fabaceae) emended based on morphology and data from nuclear and chloroplast DNA sequences. PhytoKeys 125: 1-112. https://doi.org/10.3897/phytokeys.125.34877
Figure 4 Nanhaiaspeciosa (Champ. ex Benth.) J.Compton & Schrire. A Habit B flower bud with bract and bracteole C calyx exterior and bracteole D detail of calyx exterior E detail of calyx interior F standard petal G wing petal H keel petal I staminal column J staminal column lateral view K stamen ventral and dorsal view L ovary and style M style and stigma N pod O seed lateral view P seed ventral view (all from Shiu Ling Hu 6091). Drawn by Margaret Tebbs.
Figure 2 from: Compton JA, Schrire BD, Könyves K, Forest F, Malakasi P, Mattapha S, Sirichamorn Y (2019) The Callerya Group redefined and Tribe Wisterieae (Fabaceae) emended based on morphology and data from nuclear and chloroplast DNA sequences. PhytoKeys 125: 1-112. https://doi.org/10.3897/phytokeys.125.34877
Figure 2 Distinctive morphological characters in Tribe Wisterieae. AEndosamararacemosa standard petal inner surface BPadbruggeadasyphylla standard petal inner surface CPadbruggeadasyphylla pod DPadbruggeadasyphylla seed lateral view EAustrocalleryaaustralis standard petal inner surface FAustrocalleryapilipes pod GAustrocalleryapilipes seed lateral view HPadbruggeafilipes standard petal IAfgekiasericea standard petal inner surface JAfgekiasericea seed lateral view KAfgekiasericea seed angled lateral view LCalleryanitida pod MCalleryanitida seed ventral view NCalleryanitida seed polar view OCalleryacinerea pod PWhitfordiodendronnieuwenhuisii pod QWhitfordiodendronerianthum seed RWisteriopsiseurybotrya gibbosity SWisteriopsischampionii gibbosity A from Luang Vanpruk 188 B from Scortechini 429 C, D from Lamb 395/91 E from L.J.Brass 32129 F, G from B.Gray 04319 H from Maung Po Khant 15326 I from C. Chermsirivathana 996 J, K from Mrs Collins 104/9 L–N from Theophilus SampsonO from G.Forrest 19279 P from J.P.Mogea 4182 Q from photo Y.Sirichamorn s.n..R from J. & M.S.Clemens 3637 S from Shiu Ying Hu 10476. See Appendix 1 for voucher details. Drawn by Margaret Tebbs.
Supplementary material 1 from: Compton JA, Schrire BD, Könyves K, Forest F, Malakasi P, Mattapha S, Sirichamorn Y (2019) The Callerya Group redefined and Tribe Wisterieae (Fabaceae) emended based on morphology and data from nuclear and chloroplast DNA sequences. PhytoKeys 125: 1-112. https://doi.org/10.3897/phytokeys.125.34877
: Data type: molecular data
Figure 1 from: Compton JA, Schrire BD, Könyves K, Forest F, Malakasi P, Mattapha S, Sirichamorn Y (2019) The Callerya Group redefined and Tribe Wisterieae (Fabaceae) emended based on morphology and data from nuclear and chloroplast DNA sequences. PhytoKeys 125: 1-112. https://doi.org/10.3897/phytokeys.125.34877
Figure 1 Combined Maximum Liklihood (ML) and Bayesian Inference (BI) Phylogenetic tree of Tribe Wisterieae. The tree is derived from the combined plastid and ITS, RAxML bipartitions analysis representing 77 (36) ingroup samples (taxa) and 59 (40) outgroup samples (taxa). The outgroup Schefflerodendron is used to root the trees. Lines in bold on the phylogeny incorporate results from the combined Bayesian Inference analysis, demarcating clades with BPP (0.95) support and above. Nodes are marked up with bootstrap values as percentages derived from the combined ML analysis with values of 50% or less marked in red. The collapsed portion of the tree, below the IRLC and above Schefflerodendron, represents the following genera (see Suppl. material 1: Figs S1–S6): Tribe Robinieae (Coursetia, Gliricidia, Poissonia & Poitea); Tribe Sesbanieae (Sesbania), Tribe Loteae (Coronilla, Lotus & Securigera); Tribe Millettieae (Millettia), Tribe Abreae (Abrus); Tribe Phaseoleae (Clitoria & Ophrestia); Tribe Indigofereae (Phylloxylon) and basal millettioids (Austrosteenisia, Disynstemon, Xeroderris & Platycyamus). Tribe Wisterieae is treated within five clades (Clades A–E), colour coded green for Clade A (Sarcodum, Endosamara & Sigmoidala); cyan for Clade B (Nanhaia & Wisteriopsis), red for Clade C (Callerya, Serawaia, Whitfordiodendron, Kanburia & Afgekia); orange for Clade D (Padbruggea & Austrocallerya) and yellow for Clade E (Wisteria). Each clade is further subdivided to represent the genera (except for the single accession of Serawaia which is incorporated with Whitfordiodendron in Clade C2) and E1 and E2 represent the geographical disjunction of species in Wisteria. Outgroups within the IRLC in purple include Glycyrrhiza, Adinobotrys and representatives of the Temperate Tribe block. The ingroup (IRLC) and Tribe Wisterieae are demarcated with arrows on the tree.
Figure 6 from: Compton JA, Schrire BD, Könyves K, Forest F, Malakasi P, Mattapha S, Sirichamorn Y (2019) The Callerya Group redefined and Tribe Wisterieae (Fabaceae) emended based on morphology and data from nuclear and chloroplast DNA sequences. PhytoKeys 125: 1-112. https://doi.org/10.3897/phytokeys.125.34877
Figure 6 Austrocalleryaaustralis (Endl.) J.Compton & Schrire. A Habit B leaf and detail of leaflet apex C flower buds with bract and 2 bracteoles D flower E calyx external surface F calyx detail of inner surface G standard petal inner surface H wing petal I keel petal J staminal column ventral view K stamens dorsal and ventral views L staminal column lateral view M ovary lateral view N stigma O pod P seed angled lateral view (all from Martin 1392). Drawn by Margaret Tebbs.
Figure 3 from: Compton JA, Schrire BD, Könyves K, Forest F, Malakasi P, Mattapha S, Sirichamorn Y (2019) The Callerya Group redefined and Tribe Wisterieae (Fabaceae) emended based on morphology and data from nuclear and chloroplast DNA sequences. PhytoKeys 125: 1-112. https://doi.org/10.3897/phytokeys.125.34877
Figure 3 Sigmoidalakityana (Craib) J.Compton & Schrire. A Habit B young leaf C lower surface of leaf D leaflet detail of hairs E inflorescence F flower bud with bracteole and pedicel G calyx external surface H standard petal inner surface I wing petal J keel petal K staminal column lateral view L staminal column ventral view M stamen dorsal and ventral views N ovary lateral view O style and stigma P pod Q pod detail of surface R seed ventral view S seed lateral view (all from Clark 245). Drawn by Margaret Tebbs.
Plate 2 from: Compton JA, Schrire BD, Könyves K, Forest F, Malakasi P, Mattapha S, Sirichamorn Y (2019) The Callerya Group redefined and Tribe Wisterieae (Fabaceae) emended based on morphology and data from nuclear and chloroplast DNA sequences. PhytoKeys 125: 1-112. https://doi.org/10.3897/phytokeys.125.34877
Plate 2 Afgekia, Sarcodum and Padbruggea. AAfgekiamahidoliae, Thailand, Sai Yok distr. Kanchanaburi, Y.Sirichamorn s.n.. B, CAfgekiasericea Thailand S.Mattapha 1158DSarcodumscandens Vietnam, Quang Binh Prov. Lôc & Quang P11554EAfgekiamahidiliae Thailand, Sai Yok distr. Kanchanaburi Y.Sirichamorn s.n.. FSarcodumscandens Vietnam, Quang Binh Prov. Lôc & Quang P11554GSarcodumscandens Laos, Sop Teuang, Bolikhamxai Prov. S.Lanorsavanh 1299H, IPadbruggeafilipes Thailand, Chiang Mai, Y.Sirichamorn & S.Mattapha YSM2017-1.
Figure 2 in Inferring phylogenetic relationships in the common vole (Microtus arvalis) based on mitochondrial and nuclear sequence diversities
Figure 2. Median-joining network obtained from CYTB haplotypes of Anatolian, Asian and European populations of M. arvalis. Number of mutations are shown by black lines on the branches.
FIGURE 6 in Senecio kumaonensis (Asteraceae, Senecioneae) is a Synotis based on evidence from karyology and nuclear ITS/ETS sequence data
FIGURE 6. Distribution of Synotis penninervis (= Senecio kumaonensis) (●).
Data from: Efficient detection of novel nuclear markers for Brassicaceae by transcriptome sequencing
The lack of DNA sequence information for most non-model organisms impairs the design of primers that are universally applicable for the study of molecular polymorphisms in nuclear markers. Next-generation sequencing (NGS) techniques nowadays provide a powerful approach to overcome this limitation. We present a flexible and inexpensive method to identify large numbers of nuclear primer pairs that amplify in most Brassicaceae species. We first obtained and mapped NGS transcriptome sequencing reads from two of the distantly related Brassicaceae species, Cardamine hirsuta and Arabis alpina, onto the Arabidopsis thaliana reference genome, and then identified short conserved sequence motifs among the three species bioinformatically. From these, primer pairs to amplify coding regions (nuclear protein coding loci, NPCL) and exon-primed intron-crossing sequences (EPIC) were developed. We identified 2,334 universally applicable primer pairs, targeting 1,164 genes, which provide a large pool of markers as readily usable genomic resource that will help addressing novel questions in the Brassicaceae family. Testing a subset of the newly designed nuclear primer pairs revealed that a great majority yielded a single amplicon in all of the 30 investigated Brassicaceae taxa. Sequence analysis and phylogenetic reconstruction with a subset of these markers on different levels of phylogenetic divergence in the mustard family were compared with previous studies. The results corroborate the usefulness of the newly developed primer pairs, e.g., for phylogenetic analyses or population genetic studies. Thus, our method provides a cost-effective approach for designing nuclear loci across a broad range of taxa and is compatible with current NGS technologies.
FIGURE 8. Portion B4 in Phylogenetic relationships in Brazilian Pleurothallis sensu lato (Pleurothallidinae, Orchidaceae): evidence from nuclear ITS rDNA sequences
FIGURE 8. Portion B4 (notably Specklinia) of the most parsimonious tree presented in Fig. 1.
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