Field trials in Europe with Miscanthus over the past 25 years have demonstrated that interspecies hybrids such as M. 9 giganteus (M 9 g) combine both high yield potentials and low inputs in a wide range of soils and climates. Miscanthus hybrids are expected to play a major role in the provision of perennial lignocellulosic biomass across much of Europe as part of a lower carbon economy. However, even with favourable policies in some European countries, uptake has been slow. M 9 g, as a sterile clone, can only be propagated vegetatively, which leads to high establishment costs and low multiplication rates. Consequently, a decade ago, a strategic decision to develop rapidly multiplied seeded hybrids was taken. To make progress on this goal, we have (1) harnessed Correspondence: John Clifton-

In order to elucidate the past distribution and colonization routes of broad-leaved evergreen (lucidophyllous) forests, we investigated the intraspecific phylogeographic patterns of lucidophyllous forests in Japan and surrounding areas. We selected 6 component species with a similar geographic distributions growing in Castanopsis-dominant forests. We defined possible important refugia during the glacial periods as the regions rich in rare haplotypes (with a frequency of 5% or less), or as regions rich in the number of common haplotypes (with a frequency of more than 5%). We then located the sites of refuge by comparing the intraspecific phylogeographic patterns among 6 component species of lucidophyllous forests with respect to these two parameters (i.e., haplotype uniqueness and the number of haplotypes). The following results were obtained during the course of this study: (1) rare haplotypes were distributed among islands around the main islands of Japan; (2) rare subtypes and the greatest numbers of common haplotypes were observed in Kyushu, a finding which agreed with fossilized pollen data demonstrative of the past existence of refugia in southern Kyushu; and (3) rare haplotypes were found on the Muroto Peninsula, and the second greatest numbers of common haplotypes were observed on the Kii Peninsula, a finding which suggested the existence of additional important refugia along the Pacific coast of Japan during the glacial ages.

BackgroundSubtribe Orchidinae (Orchidaceae, Orchidoideae) are a nearly cosmopolitan taxon of terrestrial orchids, comprising about 1800 species in 47 to 60 genera. Although much progress has been made in recent years of phylogenetics of Orchidinae, considerable problems remain to be addressed. Based on molecular phylogenetics, we attempt to illustrate the phylogenetic relationships and discuss generic delimitation within Orchidinae. Seven DNA markers (five plastid and two nuclear), a broad sampling of Orchidinae (400 species in 52 genera) and three methods of phylogenetic analysis (maximum likelihood, maximum parsimony and Bayesian inference) were used.ResultsOrchidinae s.l. are monophyletic. Satyrium is sister to the rest of Orchidinae s.l. Brachycorythis and Schizochilus are successive sister to Asian-European Orchidinae s.s. Sirindhornia and Shizhenia are successive sister to clade formed by Tsaiorchis-Hemipilia-Ponerorchis alliance. Stenoglottis is sister to the Habenaria-Herminium-Peristylus alliance. Habenaria, currently the largest genus in Orchidinae, is polyphyletic and split into two distant clades: one Asian-Australian and the other African–American–Asian. Diplomeris is sister to Herminium s.l. plus Asian-Australian Habenaria.ConclusionsWe propose to recognize five genera in the Ponerorchis alliance: Hemipilia, Ponerorchis s.l., Sirindhornia, Shizhenia and Tsaiorchis. Splitting Habenaria into two genera based on morphological characters and geographical distribution may be the least disruptive approach, and it is reasonable to keep Satyrium in Orchidinae.Electronic supplementary materialThe online version of this article (10.1186/s12870-017-1160-x) contains supplementary material, which is available to authorized users.

Miscanthus sinensis (Poaceae) is typical of many dominant grasses of East Asia. Due to its characteristics of fast growth and high biomass, Miscanthus, a C4 plant, has been long explored for the potential usage as biofuel. In this study, we described the development of nine microsatellite loci from M. sinensis for genetic studies. These new markers were tested in 25 individuals of five populations in three varieties. The number of alleles ranged from 3 to 8. The expected (H E ) and observed (H O ) heterozygosities were 0.37-0.78 and 0.05-0.52, respectively. All microsatellite loci are significantly deviated from Hardy-Weinberg expectations likely due to the population structure within samples. Linkage disequilibrium between four loci pairs were observed from the total 36 pairwise comparisons of loci. Cross-species transferability revealed that all loci can be applied to its closely related species, M. floridulus.

Ludwigia, a genus with rampant interspecific hybridization, is an ideal model for examining the impact of gene introgression and polyploidization on species diversification. We examined the evolution of the Ludwigia sect. Isnardia, which is a polyploid complex (x = 8) of five species distributed in North America. The phylogeny of L. sect. Isnardia was reconstructed based on sequences of cpDNA atpB­rbcL intergenic spacer and nrITS (internal transcribed spacer). Most L. sect. Isnardia species are polyphyletic at both loci, indicating possible recurrent hybridization, based on maximum likelihood trees rooted at L. sect. Microcarpium. A minimum spanning network was also constructed to examine genealogical relationships among haplotypes. In the cpDNA network, haplotypes of tetraploid L. spathulata are nested at the most interior nodes, suggesting a parental genome origin of an extinct diploid or an unsampled extant diploid with a DD cytotype. Allopolyploid L. arcuata contributed its cpDNA to hexaploid L. repens and L. brevipes. ITS haplotypes of diploid L. palustris were clustered with L. spathulata, suggesting L. palustris as the paternal genome donor. Ludwigia brevipes may have arisen via bi3directional hybridization between L. palustris and L. arcuata followed by polyploidy. Genetic and phylogenetic analyses using molecular markers with different inheritance modes provided sufficient insights into the reticulate evolution of the species of L. sect. Isnardia. Interspecific hybridization and polyploidy play a key role in the species evolution in L. sect. Isnardia.

Genus Rubus represents the second largest genus of the family Rosaceae in Taiwan, with 41 currently recognized species across three subgenera (Chamaebatus, Idaoeobatus, and Malochobatus). Despite previous morphological and cytological studies, little is known regarding the overall phylogenetic relationships among the Rubus species in Taiwan, and their relationships to congeneric species in continental China. We characterized eight complete plastomes of Taiwan endemic Rubus species: subg. Idaeobatus (R. glandulosopunctatus, R. incanus, R. parviaraliifolius, R rubroangustifolius, R. taitoensis, and R. taiwanicolus) and subg. Malachobatus (R. kawakamii and R. laciniastostipulatus) to determine their phylogenetic relationships. The plastomes were highly conserved and the size of the complete plastome sequences ranged from 155,566 to 156,236 bp. The overall GC content ranged from 37.0 to 37.3%. The frequency of codon usage showed similar patterns among species, and 29 of the 73 common protein-coding genes were positively selected. The comparative phylogenomic analysis identified four highly variable intergenic regions (rps16/trnQ, petA/psbJ, rpl32/trnL-UAG, and trnT-UGU/trnL-UAA). Phylogenetic analysis of 31 representative complete plastomes within the family Rosaceae revealed three major lineages within Rubus in Taiwan. However, overall phylogenetic relationships among endemic species require broader taxon sampling to gain new insights into infrageneric relationships and their plastome evolution.

Taxus sumatrana (Miq.) de Laub. (Taxaceae) is an endangered conifer with a scattered distribution in central Taiwan. In this study, we described the development of 12 microsatellite loci in T. sumatrana for genetic studies. These new markers were tested in nine individuals of the rare species. The number of alleles ranged from 3 to 13 and expected heterozygosity from 0.627 to 0.948. Eleven of twelve loci are significantly deviated from Hardy-Weinberg expectations due to the heterozygote deficiency.

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