Phylogenetic analysis of Saccharum s.l. (Poaceae; Andropogoneae), with emphasis on the circumscription of the South American species (original) (raw)
Related papers
A search for markers of sugarcane evolution
Genetics and Molecular Biology, 2001
To determine the phylogenetic relationship between sugarcane cultivars and other members of the Saccharinae subtribe, we identified the fast evolving ITS1-5.8S-ITS2 (ITS = internal transcribed spacer; 5.8S = 5.8S ribosomal DNA) region of the sugarcane genome in the Sugarcane Expressed Sequence Tag (SUCEST) genome project database. Parsimony analysis utilizing this region and homologs belonging to the 23 closely related Andropogoneae currently deposited in the GenBank database has shown sugarcane as the sister group of Saccharum sinense. However, because there are few parsimony-informative characters and high homoplasy in the ITS1-5.8S-ITS2 region we were not able to determine with confidence the phylogenetic relationship between sugarcane and some of the remaining members of Saccharine subtribe. To find alternatives for the phylogenetic reconstruction of sugarcane evolutionary history, we selected 17 markers (nuclear, chloroplastic or mitochondrial) from the SUCEST database of which apha-tubulin, ribosomal protein L16 (rpl16) and DNA-directed RNA polymerase beta chain (rpoC2) were found to have a low incidence of polymorphism and comparable, or even faster, rates of evolution than the ITS1-5.8S-ITS2 region. We suggest that these markers should be considered as preferential choices for phylogenetic studies of Saccharinae subtribe.
Comparative mapping of Andropogoneae: Saccharum L. (sugarcane) and its relation to sorghum and maize
Proceedings of the National Academy of Sciences, 1997
Comparative genetic maps of Papuan Saccharum officinarum L. (2n ؍ 80) and S. robustum (2n ؍ 80) were constructed by using single-dose DNA markers (SDMs). SDM-framework maps of S. officinarum and S. robustum were compared with genetic maps of sorghum and maize by way of anchor restriction fragment length polymorphism probes. The resulting comparisons showed striking colinearity between the sorghum and Saccharum genomes. There were no differences in marker order between S. officinarum and sorghum. Furthermore, there were no alterations in SDM order between S. officinarum and S. robustum. The S. officinarum and S. robustum maps also were compared with the map of the polysomic octoploid S. spontaneum 'SES 208' (2n ؍ 64, x ؍ 8), thus permitting relations to homology groups (''chromosomes'') of S. spontaneum to be studied. Investigation of transmission genetics in S. officinarum and S. robustum confirmed preliminary results that showed incomplete polysomy in these species. Because of incomplete polysomy, multipledose markers could not be mapped for lack of a genetic model for their segregation. To coalesce S. officinarum and S. robustum linkage groups into homology groups (composed of homologous pairing partners), they were compared with sorghum (2n ؍ 20), which functioned as a synthetic diploid. Groupings suggested by comparative mapping were found to be highly concordant with groupings based on highly polymorphic restriction fragment length polymorphism probes detecting multiple SDMs. The resulting comparative maps serve as bridges to allow information from one Andropogoneae to be used by another, for breeding, ecology, evolution, and molecular biology.
Journal of Plant Research, 2002
DNA sequences were used to assess the monophyly and inter-relationships of Miscanthus, Saccharum and related genera in the Saccharum complex. Three DNA regions were sequenced, including the trnL intron and the trnL-F intergenic spacer of the plastid genome and the ITS region of nuclear ribosomal DNA (nrDNA). Because it was more variable, the ITS region proved most suitable for phylogenetic reconstruction at this level, and the results indicate that Miscanthus s.l. and Saccharum s.l. are polyphyletic. A set of species from Saccharum section Ripidium (clade a) do not group closely with any members of Saccharum s.l.. A number of Miscanthus species from eastern or south-eastern Asia represent a monophyletic group with a basic chromosome number of 19 (clade b), but the other species from Africa and the Himalayas are clearly excluded. There is support for a monophyletic Saccharum s.s. clade including S. officinarum and S. spontaneum that is sister to Miscanthus s.s (clade c). There is no evidence to support the division of some Saccharum s.l. into the genera currently known as Erianthus and Narenga. Saccharum contortum (=Erianthus contortus), S. narenga (=Narenga porphyrocoma) and Erianthus rockii, group more closely with Miscanthus fuscus, a species from the Himalayas and also with the African Miscanthus s.l. species (=Miscanthidium, clade d).
Phylogeny of Andropogoneae Inferred from Phytochrome B, GBSSI, and ndhF
International Journal of Plant Sciences, 2002
Andropogoneae is a monophyletic tribe of 85 genera that includes Zea and Sorghum. All members exhibit C 4 photosynthesis and have inflorescences of paired spikelets. Previous studies of the chloroplast gene ndhF and the nuclear gene GBSSI identified numerous mutations that distinguish genera of the tribe but do not indicate relationships among them; the deep branches of the trees are quite short. Here we add newly collected data from phytochrome B to the data from the other two genes. The same pattern holds, with very short branches along the backbone of the tree indicating that the tribe resulted from rapid radiation. The phylogeny shows a single origin of a disarticulating rachis, which is a synapomorphy for the tribe. We find strong support for a core Andropogoneae that includes Andropogon, Bothriochloa, Capillipedium, Cymbopogon, Dichanthium, Heteropogon, Hyparrhenia, and Schizachyrium and support for its relationship with an expanded Saccharinae that includes Microstegium. The combined data reject the monophyly of subtribes Andropogoninae and Anthistiriinae and provide evidence that subtribes Sorghinae, Saccharinae, and Rottboelliinae are paraor polyphyletic, as is the traditional Maydeae. A relationship with Zea and Tripsacum is indicated for Elionurus, while Chionachne and Phacelurus are shown to diverge early in the history of the tribe. Arundinella hirta and Arundinella nepalensis can be included in an expanded Andropogoneae.
Comparative genome mapping of sugar cane with other species within the Andropogoneae tribe
Heredity, 1994
Comparative mapping within the tribe Andropogoneae has recently progressed with the development of mapped maize genomic probes that can be used for sorghum and sugar cane genomes. In the present study, data from previous reports were used to locate various linkage groups of sugar cane and sorghum on the genomic map of maize. Syntenic genome regions in the three plants were determined according to existing bridge-loci. The distribution of these synteny clusters closely matched the duplication pattern in maize. In several cases, the two arms of a single maize chromosome corresponded to at least two synteny clusters. There seem to be common chromosome rearrangements between maize and sugar cane and between maize and sorghum. In this respect, sugar cane and sorghum appear to be more closely related than either one with maize. A more detailed analysis of two synteny clusters was undertaken using recent sugar cane data to compare gene orders and recombination rates of the three plants. The three genomes showed colinearity in these regions. Distances between genes were similar in maize and sorghum, whereas sugar cane tended to display less recombination, at least in the varietal progeny investigated.
Darwiniana
El complejo Andropogon lateralis está constituido por alrededor de 13 entidades taxonómicas: siete especies y seis híbridos inter-específicos distribuidos en Centro y Sudamérica. Los híbridos naturales en este grupo son frecuentes debido a la ausencia de barreras reproductivas entre las especies. Estos híbridos han sido recolectados en los últimos dos siglos y, en la mayoría de los casos, han llamado la atención de los taxónomos, quienes han descrito a varias de estas combinaciones formalmente como nuevos taxones. Por lo tanto, las entidades taxonómicas basadas en combinaciones híbridas han sido válidamente publicadas. De las diez entidades taxonómicas que integran el complejo A. lateralis en el Cono Sur de Sudamérica, cinco corresponden a híbridos naturales y tres de estos poseen nombres legítimos (A. × coloratus, A. × lindmanii y A. × subtilior). Sobre la base de análisis morfométricos y estudios previos, proponemos que los dos híbridos naturales restantes también merecen nombres taxonómicamente válidos. Estas entidades son Andropogon × velutinus (A. bicornis × A. glaziovii, = Andropogon sp 1 de acuerdo a Zanin, 2001) y Andropogon × catarinensis (A. bicornis × A. arenarius). En este trabajo se presentan los tratamientos taxonómicos de Andropogon × velutinus y Andropogon × catarinensis. Palabras clave. Análisis multivariado; Andropogoneae; híbridos interespecíficos; morfometría; taxonomía. Original recibido el 2 de abril de 2012, aceptado el 2 de junio de 2012. Resumen. Nagahama, N.; A. M. Anton, M. I. Hidalgo & G. A. Norrmann. 2012. Nombres válidos para híbridos del complejo Andropogon lateralis (Poaceae, Andropogoneae) sobre la base de análisis multivariados. Darwiniana 50(1): 114-123.
2007
Phylogenetic relationships among 85 species representing 35 genera in the grass tribe Andropogoneae were estimated from maximum parsimony and Bayesian analyses of nuclear ITS and chloroplast trnL-F DNA sequences. Ten of the 11 subtribes recognized by Clayton and Renvoize (1986) were sampled. Independent analyses of ITS and trnL-F yielded mostly congruent, though not well resolved, topologies. Arundinella is sister to Andropogoneae in the trnL-F phylogeny and is nested within the tribe in the ITS and combined data trees. Tristachya is sister to Andropogoneae ϩ Arundinella in the ITS phylogeny. Four clades are common to the ITS and trnL-F phylogenies and the trees from the combined data set. Clade A consists of Andropogon, Diectomis, Hyparrhenia, Hyperthelia, and Schizachyrium. Within this clade, Andropogon distachyos, Hyparrhenia, and Hyperthelia form clade C. Clade B consists of Bothriochloa, Capillipedium, and Dichanthium, and clade D includes Chrysopogon and Vetiveria. Analysis of the combined data resulted in an unsupported larger clade comprising clades A and B plus Cymbopogon, and a sister clade of Heteropogon, Iseilema, and Themeda. This larger clade is similar to the core Andropogoneae clade previously reported (Spangler et al. 1999; Mathews et al. 2002). Based on our sample, which represents 41% of the tribe's genera, most of Clayton and Renvoize's (1986) subtribes are not monophyletic.
Phylogenetic analysis of organellar DNA sequences in the Andropogoneae: Saccharinae
Theoretical and Applied Genetics, 1994
To study the phylogenetics of sugarcane (Saccharum officinarum L.) and its relatives we sequenced four loci on cytoplasmic genomes (two chloroplast and two mitochondrial) and analyzed mitochondrial RFLPs generated using probes for COXI, COXII, COXIII, Cob, 18S+5S, 26S, ATPase 6, ATPase 9, and ATPase ~ (D'Hont et al. 1993). Approximately 650 bp of DNA in the intergenic spacer region between rbcL and atpB and approximately 150 bp from the chloroplast 16S rDNA through the intergenic spacer region tRNA val gene were sequenced. In the mitochondrial genome, part of the 18S rRNA gene and approximately 150 bp from the 18S gene 3' end, through an intergenic spacer region, to the 5S rRNA gene were sequenced. No polymorphisms were observed between maize, sorghum, and 'Saccharum complex' members for the mitochondrial 18S internal region or for the intergenic tRNA va~ chloroplast locus. Two polymorphisms (insertiondeletion events, indels) were observed within the 18S-5S mitochondrial locus, which separated the accessions into three groups: one containing all of the Erianthus, Eccoilopus, Imperata, Sorghum, and 1 Miscanthus species; a second containing Saccharum species, Narenga porphyrocoma, Sclerostachya fusca, and 1 presumably hybrid Miscanthus sp. from New Guinea; and a third containing maize. Eighteen accessions were sequenced for the intergenic region between rbcL and atpB, which was the most polymorphic of the regions studied and contained 52 site mutations and 52 indels, across all taxa. Within the Saccharum complex, at most 7 site mutations and 16 indels were informative. The maternal lineage of Erianthus/Eccoilopus was nearly as divergent from the remaining Saccharum complex members as it was from sorghum, in agreement with a previous study. Sequences from the rbcL-atpB spacer were aligned with GENBANK sequences for Communicated by A
Andropogon × paraguariensis, un nuevo nombre para Andropogon × velutinus (Poaceae, Andropogoneae)
2015
Se propone el nuevo nombre, Andropogon × paraguariensis Norrmann & Nagahama para reemplazar al nombre ilegítimo Andropogon × velutinus Norrmann & Nagahama, un híbrido natural del cono sur de SudaméricaThe new name Andropogon × paraguariensis Norrmann & Nagahama is proposed to replace the illegitimate name Andropogon × velutinus Norrmann & Nagahama, a natural hybrid from southern South America.Fil: Nagahama, Nicolas. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Anton, Ana Maria Ramona. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Inst...
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.