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64 results for “chloroplast sequence”
Data from: Phylogeographical patterns of an alpine plant, Rhodiola dumulosa (Crassulaceae), inferred from chloroplast DNA sequences
The phylogeographical patterns of Rhodiola dumulosa, an alpine plant species restrictedly growing in the crevices of rock piles, were investigated based on 4 fragments of the chloroplast genome. To cover the full distribution of R. dumulosa in China, 19 populations from 3 major disjunct distribution areas (northern, central, and northwestern China) were sampled. A total of 5881bp (after alignment) of chloroplast DNA (cpDNA) from 100 individuals were sequenced. The combined cpDNA data set yielded 36 haplotypes. The total genetic diversity of R. dumulosa was remarkably high (H T = 0.981). The interpopulation genetic differentiation was significantly large (F ST = 0.8537, P < 0.001), possibly due to the long-term isolation of the natural populations. N ST was significantly larger than G ST (P < 0.001), indicating the presence of phylogeographical structure among the R. dumulosa populations. We propose 2 migration steps to explain the current distribution of R. dumulosa in China. First, this species migrated from refugia in the Qinghai-Tibetan Plateau to northern areas via the intervening highlands when temperatures increased; second, the highland populations migrated toward the mountaintops when temperatures increased further because R. dumulosa is adapted to cold environments. During the second migration step, the common ancestral haplotypes may have been gradually lost.
Molecular systematics of the tribe Physarieae (Brassicaceae) based on the nuclear ITS, LUMINIDEPENDENS, and chloroplast ndhF: Sequence alignments, trees, and supplemental figures
<p>Physarieae is a small tribe of herbaceous annual and woody perennial mustards that are mostly endemic to North America, with its members including a large amount of variation in floral, fruit and chromosomal variation. Building on a previous study of Physarieae based on morphology and <i>ndhF</i> plastid DNA, we reconstructed the evolutionary history of the tribe using new sequence data from two nuclear markers, and compared the new topologies against previously published cpDNA-based phylogenetic hypotheses. The novel analyses included ca. 420 new sequences of ITS and <i>LUMINIDEPENDENS</i> (<i>LD</i>) markers for 39 and 47 species, respectively, with sampling accounting for all seven genera of Physarieae, including nomenclatural type species, and 11 outgroup taxa. Maximum parsimony, maximum likelihood, and Bayesian analyses showed that these additional markers were largely consistent with the previous <i>ndh</i>F data that supported the monophyly of Physarieae and resolved two major clades within the tribe, i.e. DDNLS (<i>Dithyrea</i>, <i>Dimorphocarpa</i>, <i>Nerisyrenia</i>, <i>Lyrocarpa</i>, and <i>Synthlipsis</i>) and PP (<i>Paysonia</i> and <i>Physaria</i>). New analyses also increased internal resolution for some closely related species and lineages within both clades. The monophyly<i> </i>of <i>Dithyrea</i> and the sister relationship of <i>Paysonia</i> to <i>Physaria</i> was consistent in all trees, with the sister relationship of <i>Nerisyrenia </i>to <i>Lyrocarpa </i>supported by <i>ndhF</i> and <i>ITS</i>, and the positions of <i>Dimorphocarpa</i> and <i>Synthlipsis</i> shifted within the DDNLS Clade depending on the employed data set. Finally, using the strong, new phylogenetic framework of combined cpDNA + nDNA data, we discussed standing hypotheses of trichome evolution in the tribe suggested by <i>ndhF</i>.</p>
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.
Supplementary material 1 from: Li Z, Huang Z, Wan X, Yu J, Dong H, Zhang J, Zhang C, Wang S (2023) Complete chloroplast genome sequence of Rhododendron mariesii and comparative genomics of related species in the family Ericaeae. Comparative Cytogenetics 17: 163-180. https://doi.org/10.3897/compcytogen.17.101427
Taxonomic and accession information on cp genomes downloaded from NCBI database
Data from: Timing transantarctic disjunctions in the Atherospermataceae (Laurales): evidence from coding and noncoding chloroplast sequences
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Data from: Phylogeographical patterns of an alpine plant, Rhodiola dumulosa (Crassulaceae), inferred from chloroplast DNA sequences
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Data from: Mating systems and selection efficacy: a test using chloroplastic sequence data in Angiosperms
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Data from: Congruent deep relationships in the grape family (Vitaceae) based on sequences of chloroplast genomes and mitochondrial genes via genome skimming
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Data from: Chloroplast phylogenomic data from the green algal order Sphaeropleales (Chlorophyceae, Chlorophyta) reveal complex patterns of sequence evolution
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Molecular systematics of the tribe Physarieae (Brassicaceae) based on the nuclear ITS, Luminidependens, and chloroplast ndhF: Sequence alignments, trees, and supplemental figures
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Chloroplast genome sequencing reads from sweet potato
<p>Tutorial data for chloroplast genome assembly: fastq reads from illumina and nanopore sequencing for the sweet potato.</p> <p>Data from: Zhou C, Duarte T, Silvestre R et al. 2018 (https://doi.org/10.12688/gatesopenres.12856.1), hosted at EBI ENA under accession numbers: illumina (SRR6828568) and nanopore (SRR6828567).</p> <p>This is how the files have been changed from the original datasets: </p> <p>illumina-reduced: has the first 62,500 reads only</p> <p>illumina-tiny: has the first 12,500 reads only</p> <p>nanopore-reduced: has the first 2,000 reads only</p> <p>nanopore-tiny: has the first 250 reads only</p> <p> </p>
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