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91 results for “chloroplast genome”
Data from: Distinctive architecture of the chloroplast genome in the chlorodendrophycean green algae Scherffelia dub and Tetraselmis sp. CCMP 881
The Chlorodendrophyceae is a small class of green algae belonging to the core Chlorophyta, an assemblage that also comprises the Pedinophyceae, Trebouxiophyceae, Ulvophyceae and Chlorophyceae. Here we describe for the first time the chloroplast genomes of chlorodendrophycean algae (Scherffelia dubia, 137,161 bp; Tetraselmis sp. CCMP 881, 100,264 bp). Characterized by a very small single-copy (SSC) region devoid of any gene and an unusually large inverted repeat (IR), the quadripartite structures of the Scherffelia and Tetraselmis genomes are unique among all core chlorophytes examined thus far. The lack of genes in the SSC region is offset by the rich and atypical gene complement of the IR, which includes genes from the SSC and large single-copy regions of prasinophyte and streptophyte chloroplast genomes having retained an ancestral quadripartite structure. Remarkably, seven of the atypical IR-encoded genes have also been observed in the IRs of pedinophycean and trebouxiophycean chloroplast genomes, suggesting that they were already present in the IR of the common ancestor of all core chlorophytes. Considering that the relationships among the main lineages of the core Chlorophyta are still unresolved, we evaluated the impact of including the Chlorodendrophyceae in chloroplast phylogenomic analyses. The trees we inferred using data sets of 79 and 108 genes from 71 chlorophytes indicate that the Chlorodendrophyceae is a deep-diverging lineage of the core Chlorophyta, although the placement of this class relative to the Pedinophyceae remains ambiguous. Interestingly, some of our phylogenomic trees together with our comparative analysis of gene order data support the monophyly of the Trebouxiophyceae, thus offering further evidence that the previously observed affiliation between the Chlorellales and Pedinophyceae is the result of systematic errors in phylogenetic reconstruction.
Comparison among the chloroplast genomes of five species of Chamaerhodos (Rosaceae: Potentilleae): phylogenetic implications
<p><em>Chamaerhodos</em> is a small genus with ca 7–8 species with a disjunct distribution in Asia and western North America. Due to limited sampling of species and genes in previous studies, little is known about the phylogenetic relationships among the species. Moreover, chloroplast genomic resources for <em>Chamaerhodos</em> have been limited. Herein, we conducted a comparative analysis of the complete chloroplast (cp) genomes of five <em>Chamaerhodos</em> species. The five cp genomes had a typical quadripartite structure with high conservation of gene content and gene order. These five cp genomes encoded an identical set of 129 genes, including 84 protein-coding genes, 37 tRNA genes and eight rRNA genes. Comparison of the boundaries between the IRs and single copy regions revealed only very slight boundary differences and the five cp genomes showed only little sequence divergence. Seven regions (<em>trnR-UCU-atpA</em>,<em> trnS-GCU- trnG-UCC</em>, <em>TrnG-GCC-trnfM-CAU</em>, <em>trnL-UAA</em> intron, <em>trnH-GUG-psbA</em>, <em>trnF-GAA- ndhJ</em>, <em>matK-5′-trnK-UUU</em>) were identified as excellent candidate markers. A total of 117, 108, 116, 117 and 118 perfect SSRs were detected in the cp genomes of <em>Ch. altaica</em>, <em>Ch. canescens</em>, <em>Ch. erecta</em>, <em>Ch. sabulosa</em> and <em>Ch. trifida</em>, respectively. A phylogenetic analysis support the monophyly of <em>Chamaerhodos</em> and place it as part of the Fragariinae clade sister to the clade of <em>Dasiphora</em>, <em>Drymocallis</em> and <em>Potaninia</em>. Within <em>Chamaerhodos</em>, <em>Ch. canescens</em> was inferred sister to a clade containing the other four species. The detailed characterization of the <em>Chamaerhodos</em> chloroplast genomes sets the foundation for further studies on the genus and its close relatives in the economically important Rosaceae.</p>
Characterization of the complete chloroplast genome of the medicinal herb Veronica polita Fr. (Lamiales: Plantaginaceae)
<p><em>Veronica polita</em> Fr. (synonym: <em>Veronica didyma</em> Ten.), an annual herbaceous species with high medicinal values, is originally from Southwest Asia but has been naturalized widely in many regions of the world. In this study, the complete chloroplast genome of <em>V. polita</em> was determined to be 150,191 bp long with a typical quadripartite structure. It encodes a panel of 114 genes with 18 of them being completely or partially duplicated and 19 of them possessing one or two introns. The phylogenetic analysis appeared to support the tribal-level taxonomy of the family Plantaginaceae, and revealed that <em>V. polita</em> was most closely related to the congener <em>V. persica</em>.</p>
The complete chloroplast genome of Pedicularis rudis Maxim. (Lamiales: Orobanchaceae), a perennial herb endemic to China
<p><em>Pedicularis rudis</em> Maxim. is a species of perennial herb endemic to China. In this study, the complete chloroplast genome of <em>P. rudis</em> was determined to be 151,443 bp long with a typical quadripartite structure, comprising two inverted repeat regions (IRa and IRb, 25,719 bp each), a large single-copy (LSC) region (83,119 bp) and a small single-copy (SSC) region (16,886 bp). It encodes a panel of 110 genes with 19 of them being completely or partially duplicated and 18 of them possessing one or two introns. Phylogenetic analysis revealed that <em>P. rudis</em> was most closely related to the congener <em>P. shansiensis</em>.</p>
FIGURE 7 in Indocalamus chongzhouensis (Poaceae: Bambusoideae), a new synonym of I. emeiensis: evidence from morphology and complete chloroplast genome data
FIGURE 7. Geographical distribution of Indocalamus emeiensis (red pentacles).
Data from: Whole chloroplast genome and gene locus phylogenies reveal the taxonomic placement and relationship of Tripidium (Panicoideae: Andropogoneae) to sugarcane
Background: For over 50 years, attempts have been made to introgress agronomically useful traits from Erianthus sect. Ripidium (Tripidium) species into sugarcane based on both genera being part of the 'Saccharum Complex', an interbreeding group of species believed to be involved in the origins of sugarcane. However, recent low copy number gene studies indicate that Tripidium and Saccharum are more divergent than previously thought. The extent of genus Tripidium has not been fully explored and many species that should be included in Tripidium are still classified as Saccharum. Moreover, Tripidium is currently defined as incertae sedis within the Andropogoneae, though it has been suggested that members of this genus are related to the Germainiinae. Results: Eight newly-sequenced chloroplasts from potential Tripidium species were combined in a phylogenetic study with 46 members of the Panicoideae, including seven Saccharum accessions, two Miscanthidium and three Miscanthus species. A robust chloroplast phylogeny was generated and comparison with a gene locus phylogeny clearly places a monophyletic Tripidium clade outside the bounds of the Saccharinae. A key to the currently identified Tripidium species is presented. Conclusion: For the first time, we have undertaken a large-scale whole plastid study of eight newly assembled Tripidium accessions and a gene locus study of five Tripidium accessions. Our findings show that Tripidium and Saccharum are eight million years divergent, last sharing a common ancestor 12 million years ago. We demonstrate that four species should be removed from Saccharum/Erianthus and included in genus Tripidium. In a genome context, we show that Tripidium evolved from a common ancestor with and extended Germainiinae clade formed from Germainia, Eriochrysis, Apocopis, Pogonatherum and Imperata. We re-define the 'Saccharum complex' to a group of genera that can interbreed in the wild and extend the Saccharinae to include Sarga along with Sorghastrum, Microstegium vimineum and Polytrias (but excluding Sorghum). Monophyly of genus Tripidium is confirmed and the genus is expanded to include Tripidium arundinaceum, Tripidium procerum, Tripidium kanashiroi and Tripidium rufipilum. As a consequence, these species are excluded from genus Saccharum. Moreover, we demonstrate that genus Tripidium is distinct from the Germainiinae.
Supplementary material 1 from: Fu L-F, Xiong C, Monro AK, Fan Q, Chen Z-X, Wen F, Xin Z-B, Wei Y-G, Liao W-B (2022) Pilea danxiaensis (Urticaceae), a new species in the Danxia landform from Guangdong, China including a description of the entire chloroplast genome. PhytoKeys 204: 109-119. https://doi.org/10.3897/phytokeys.204.86857
Appendix S1
FIGURE. Chloroplast genome maps of Strobilanthes lupulina and S. glandulata. in Strobilanthes glandulata (Acanthaceae), a new species from Sri Lanka based on the morphological and molecular evidences
FIGURE. Chloroplast genome maps of Strobilanthes lupulina and S. glandulata.
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
Evolution of Rosaceae chloroplast genomes highlights unique Cerasus diversification and independent origins of fruit cherry
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Data from: Whole chloroplast genome and gene locus phylogenies reveal the taxonomic placement and relationship of Tripidium (Panicoideae: Andropogoneae) to sugarcane
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Data from: Phylogenetic analysis of 47 chloroplast genomes clarifies the contribution of wild species to the domesticated apple maternal line
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Data from: Distinctive architecture of the chloroplast genome in the chlorodendrophycean green algae Scherffelia dub and Tetraselmis sp. CCMP 881
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Comparison among the chloroplast genomes of five species of Chamaerhodos (Rosaceae: Potentilleae): phylogenetic implications
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Data from: Different processes shape the patterns of divergence in the nuclear and chloroplast genomes of a relict tree species in East Asia
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Data from: Development of chloroplast genomic resources for Cynara
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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: Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies
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A photosynthesis operon in the chloroplast genome drives speciation in evening primroses
GEO Series GSE174154. Oenothera elata subsp. hookeri; Oenothera elata subsp. hookeri x Oenothera grandiflora. 30 samples. Type: Expression profiling by high throughput sequencing; Other.
Chloroplast redox status modulates genome-wide plant responses during plant-microbe interaction
GEO Series GSE92596. Nicotiana tabacum. 8 samples. Type: Expression profiling by array.
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