Phylogenetics of Miscanthus , Saccharum and related genera (Saccharinae, Andropogoneae, Poaceae) based on DNA sequences from ITS nuclear ribosomal DNA and plastid trnL intron and trnL-F intergenic spacers (original) (raw)
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On the Taxonomy of the Members of ‘Saccharum Complex’
Genetic Resources and Crop Evolution, 2005
The difficulty and problems encountered in the study of cultivated plants, in general and sugarcane, in particular has been indicated. In order to understand these problems, a brief review on the taxonomy of Saccharum and closely related taxa, namely, Erianthus, Sclerostachya, Narenga and Miscanthus (generally known as 'Saccharum complex') has been given. A short account on the important morphological features that are specific to sugarcane has also been stated as classification is commonly based on such morphological characters. A note has been added on the chromosome number, origin, and distribution of the species of 'Saccharum complex' members. Taxonomic keys have been devised for identification of the genera of Saccharinae and for the species of Saccharum and Erianthus occurring in India. A new combination, Sclerostachya fallax (Balansa) Amalraj et Balasundaram, has also been proposed.
Analysis of genetic diversity and phylogeny in Saccharum and related genera using RAPD markers
Genetic Resources and Crop Evolution, 1999
Molecular diversity in Saccharum complex was studied using 195 RAPD markers generated by 12 random primers. Among the Saccharum species, S. officinarum showed a low level of genetic diversity while S. sinense was found to be more diverse. Six taxonomical groups were clearly resolved in the cluster analysis. S. officinarum, S. robustum, S. spontaneum and Erianthus spp. formed discrete groups. S. barberi and S. sinense formed a single cluster, so also Narenga and Sclerostachya. S. officinarum was found to be closer to S. robustum and distant from S. spontaneum. Among the related genera, Sclerostachya was closer to Saccharum while Erianthus was found to be highly divergent from all the Saccharum species. Six of the primers used generated RAPD fragments unique to Erianthus. It is suggested that the Erianthus spp. can contribute substantially towards sugarcane varietal improvement in view of its greater divergence with Saccharum.
Phylogenetics of Ruscaceae sensu lato based on plastid rbcL and trnL-F DNA sequences
We studied the phylogeny and relationships among several families within Asparagales by analysis of trnL-F and rbcL sequences. As judged from rbcL, trnL-F or combined data, the order Asparagales is monophyletic with high bootstrap support. The classification into higher and lower asparagoids, which are characterized by successive microsporogenesis and simultaneous microsporogenesis, respectively, is only weakly supported by the trnL-F and combined data. The lower asparagoids with simultaneous microsporogenesis are clearly not monophyletic. Within Asparagales, the families Convallariaceae, Ruscaceae, Dracaenaceae and Nolinaceae are not monophyletic. This is well supported by trnL-F data and the combined analysis and moderately supported by rbcL sequences. Especially Convallariaceae are highly polyphyletic. However, the four families formed a clearly defined clade in our analysis and thus, the concept of lumping the four families into a large family Ruscaceae s. lat. received further support. Within Ruscaceae s. lat., the genus Peliosanthes does not have a fixed position. This genus occupies a position basal to the remaining taxa both in the rbcL and the combined trees, but falls into a clade together with Liriope and Ophiopogon like in traditional taxonomy in the trnL-F analysis. Both in the trnL-F and the combined trees the families Asparagaceae and Eriospermaceae are located next to Ruscaceae s. lat., but no clear sister group relationship is obvious from our data. Lumping of Eriospermaceae with Ruscaceae s. lat. is not supported by any of the molecular data sets.
Euphytica, 1997
A collection of 65 Erianthus Michx. sect. Ripidium Henrard accessions (representing seven accepted species) and 14 Saccharum L. representatives (S. officinarum L. and S. spontaneum L.) were studied by RFLP analysis using 14 dispersed nuclear single-copy probes from maize. An intergeneric distance (1–F) of 0.748 was revealed between Erianthus and Saccharum. Within the Erianthus collection, the greatest distances were found between E. elephantinus Hook f. or E. ravennae (L.) P. Beauv. (the two 2n=20 species), and the rest of the Erianthus collection. The smallest distances were found amongst the E. arundinaceus (Retz.) Jeswiet clones collected in Indonesia ((1–F)=0.005). In addition, a partition based on the geographical origin and consistent with the chromosome numbers, ie E. arundinaceus from Indonesia versus E. arundinaceus and E. procerus from India, was revealed. E. bengalense was intermediate. The study of the Saccharum individuals confirmed the greater variability of S. spontaneum compared to the so called noble cane, S. officinarum. The 2n=80 S. spontaneum genotypes were shown to be closely related to S. officinarum. The implication of these results on the involvement of S. spontaneum and Erianthus sect. Ripidium in the origin of S. officinarum is discussed.
Weed Biology and Management, 2014
Nucleotide sequence variations were investigated with respect to the geographical distribution patterns of Miscanthus sinensis populations that were sampled from 26 Japanese national parks and three populations of the Ryukyu Islands. Twelve homozygous sequences in the nuclear ribosomal DNA internal transcribed spacer region were detected. The populations of M. sinensis in mainland Japan mainly were composed of a monophyletic group with a symapomorphic character, whereas those in the Ryukyu Islands included a polyphyletic group. Only an internal transcribed spacer haplotype with a plesiomorphic character was found in both mainland Japan and the Ryukyu Islands. Thus, no clear geographical isolation was observed in this species. These facts might be caused by the ability of M. sinensis as a pioneer plant to have a high migration potential and high gene flow by outcrossing. On the basis of the results of this study (nuclear ribosomal DNA) and the previous study (chloroplast DNA), a phyl...
Contribution to the taxonomy and phylogeny of Sarcocapnos DC. (Fumariaceae)
Plant Systematics and Evolution, 2003
To solve problems concerning the status of the taxa described in the genus Sarcocapnos, we have conducted a study using morphological, pollen morphology (light microscopy), cytogenetic and molecular techniques. Focusing on the last technique, we have sequenced ITS-1 and ITS-2 of nuclear rDNA. The species differ basically according to 5 morphological traits (leaf shape, flower spur, corolla colour, corolla size, and crest of the stigmatic surface). The cytogenetic analyses indicated n ¼ 16 to be the standard chromosome number. The ITS analyses showed that the genus is monophyletic, defining two main well-supported clades, one containing S. saetabensis and S. enneaphylla, and one containing the rest of the species. In this second clade, S. speciosa, S. pulcherrima, and S. baetica subsp. ardalii are related, as are S. integrifolia, S. crassifolia subsp. crassifolia, and S. crassifolia subsp. atlantis; S. baetica subsp. baetica forms a trichotomy with the foregoing groups. S. speciosa is shown to be a species separate from S. crassifolia subsp. crassifolia, as in the case of S. baetica with respect to S. integrifolia. Palynologically, the parameters used enabled us to establish clear differences between the taxa, often corroborating the macromorphological and genetic data. The flower spur has been reduced several times in different groups of the genus, for which the classifications established on the basis of this trait are paraphyletic.
Erratum: Phylogeny of Vitaceae based on the nuclear GAI1 gene sequences
Canadian Journal of Botany, 2007
Phylogenetic analysis of 105 nuclear GAI1 sequences of Vitaceae provided a fairly robust phylogeny, largely congruent with the recently published chloroplast data of the family. In the GAI1 phylogeny, Cayratia Juss., Tetrastigma (Miq.) Planch., and Cyphostemma (Planch.) Alston form a clade. Cyphostemma and Tetrastigma are both monophyletic, and Cayratia is paraphyletic. Ampelopsis Michx is paraphyletic with the African Rhoicissus Planch. and the South American Cissus striata Ruiz & Pav. and its close relatives (e.g., Cissus simsiana Roem. & Schult.) nested within it. The pinnately leaved Ampelopsis forms a subclade, and the simple and palmately leaved Ampelopsis constitutes another subclade. All species of Cissus L. sampled from Asia, Africa, and Central and South America (except the C. striata complex) form a monophyletic group. Pterisanthes Blume of southeastern Asia forms a clade with the Asian Ampelocissus Planch. Vitis L. is monophyletic and forms a larger clade with the tropical Ampelocissus and Pterisanthes. Parthenocissus Planch., forms a clade with Yua C.L. Li, with each genus reportedly monophyletic. Cissus from the Old World is paraphyletic with the neotropical core Cissus nested within it. The basal grade of Cissus consists of taxa from Africa. The African-Asian biogeographic relationships are complex, with several intercontinental disjunctions. The Northern Hemisphere Ampelopsis is most closely related to the South American C. striata complex and the African Rhoicissus.
ALGAE, 2002
Phylogenetic relationships of Sargassum with the emphasis on subgenus Bactrophycus were examined on the basis of internal transcribed spacer (ITS) and 5.8S sequences of nuclear ribosomal DNA (rDNA) for 23 accessions of Sargassum representing 18 species, and two outgroups, Hizikia fusiformis (Harvey) Okamura and Myagropsis myagroides (Mertens ex Turner) Fensholt. Fifteen species were included in the molecular analysis to represent all sections of the subgenus Bactrophycus recognized to date (Spongocarpus, Teretia, Halochloa, and Repentia), and additional three species were analyzed to represent three other subgenera of Sargassum (Sargassum, Schizophycus, and Phyllotrichia) found in Korea. In the resulting phylogenetic trees, H. fusiformis was nested in the clade of subgenus Bactrophycus as sister group of section Teretia with high confidence even though it was designated as one of outgroups in the phylogenetic analysis. Species of section Teretia formed a very robust clade. Section Spongocarpus was branched off as a sister group of the Hizikia-Teretia clade. Members of section Halochloa showed very little differences in ITS sequences and formed a very tight clade with S. yezoense, which is a member of section Repentia (99% in bootstrap analysis). Sequences of ITS of S. yezoense was identical with ones of S. siliquastrum, although they belong to different sections, Repentia and Halochloa, respectively. In the phylogenetic analyses of ITS sequences, members of subgenus Bactrophycus including the monotypic genus Hizikia were clearly separated from other subgenera of Sargassum as forming a highly supported monophyletic group. The molecular data strongly claim that Hizikia should be treated as a member of the genus Sargassum. The molecular study also suggests that sections Repentia and Halochloa are closely allied, but further analyses with more extensive sampling should be needed to look into taxonomic circum criptions for sections Halochloa and Repentia, of which taxonomic limitations were not clearly defined in this study.