The diploid Oryza species with C-genome type possesses abundant genes useful for rice improvement and provides parental donors of many tetraploid species with the C-genome (BBCC, CCDD). Despite extensive studies, the phylogenetic relationship among the C-genome species and the taxonomic status of some taxa remain controversial. In this study, we reconstructed the phylogeny of three diploid species with C-genome (Oryza officinalis, O. rhizomatis, and O. eichingeri) based on sequences of 68 nuclear single-copy genes. We obtained a fully resolved phylogenetic tree, clearly indicating the sister relationship of O. officinalis and O. rhizomatis, with O. eichingeri being the more divergent lineage. Incongruent phylogenies of the C-genome species found in previous studies might result from lineage sorting, introgression/hybridization and limited number of genetic markers used. We further applied a recently developed Bayesian species delimitation method to investigate the species status of the Sri Lankan and African O. eichingeri. Analyses of two datasets (68 genes with a single sample, and 10 genes with multiple samples) support the distinct species status of the Sri Lankan and African O. eichingeri. In addition, we evaluated the impact of the number of sampled individuals and loci on species delimitation. Our simulation suggests that sampling multiple individuals is critically important for species delimitation, particularly for closely related species.

Basal angiosperms contain a wide diversity of floral and growth forms and gave rise to the largest recent angiosperm lineages. As none of the basal angiosperm genomes has been sequenced, examining large bacterial artificial chromosome (BAC) inserts remains the main approach to providing a first glimpse of the structure and organization of their genomes. In this study, we sequenced a 126.9-kbp BAC contig harboring a cinnamyl alcohol dehydrogenase gene (LtuCAD1) in a basal angiosperm species, Liriodendron tulipifera L., an important timber tree species with significant ecological and economic values. A key enzyme in lignin biosynthesis, CAD catalyzes the final step in the synthesis of monolignols. We carried out phylogenetic analyses of seven full-length CAD family genes (LtuCAD1–7) obtained from a comprehensive Liriodendron expressed sequence tag dataset. The phylogenetic tree suggests that LtuCAD1 is the primary CAD gene involved in lignifications as it is the only Liriodendron CAD grouped with the bona fide CADs class. As well as the LtuCAD1, the BAC contig contained fragmented sequences for one integrase, eight hypothetical proteins, two gag-pol polyproteins, one RNase H family protein, and one chromatin binding protein. Comparative analysis with other angiosperm species suggests that the genomic segment in this BAC has undergone frequent arrangement. This study is our initial step in identifying and understanding lignin biosynthesis genes from basal angiosperm species. Such knowledge can help bridge the information gap between hardwood (angiosperm) and softwood (gymnosperm) species and benefit potential breeding and biotechnology application for enhanced production of biomass and digestibility in L. tulipifera.

Lindelofia longiflora (Royle ex Benth.) Baill. var. falconeri (Cl.) Brand (Family: Boraginaceae) is investigated cytologically (n= 12) for the first time from the cold deserts of Pangi Valley, Chamba District (Himachal Pradesh) in India. We report the formation of syncytes and 2n pollen grains in the species. During meiosis, the majority of the pollen mother cells (PMCs) exhibited 12 bivalents, equal segregation of chromosomes during anaphases, regular tetrads, and normal-sized pollen grain formation. Occasionally, two proximate PMCs fused during the early stages of prophase-I and resulted in the formation of syncytes. The frequency of syncytes in the accession is rather low, at 25 out of 1866 (1.33%). Such syncyte PMCs are detectable during meiosis due to their larger size compared to typical PMCs. The syncytes or polyploid cells showed normal 24 bivalents and depicted perfectly regular meiotic course. But the products of such PMCs yield 2n or larger sized pollen grains that are almost double the size of typical normal or n pollen grains. The origin of syncytes as a consequence of the fusion of meiocytes during the early stages of meiosis-I could be attributed to low temperature stress conditions prevailing in the Pangi Valley, where temperature during May and June dip to below freezing, the time the plants enters the reproductive/flowering bud stage. It is possible that such apparently fertile 2n pollen grains originating from syncytes might play a role in the origin of intraspecific polyploids in the species.

Four DNA barcoding loci, chloroplast loci rbcL, matK, trnH-psbA, and nuclear locus internal transcribed spacer (ITS), were tested for the accurate discrimination of the Chinese species of Gaultheria by using intraspecific and interspecific pairwise P-distance, Wilcoxon signed rank test, and tree-based analyses. This study included 186 individuals from 89 populations representing 30 species. For all individuals, single locus markers showed high levels of sequencing universality but were ineffective for species resolvability. Polymerase chain reaction amplification and sequencing were successful for all four loci. Both ITS and matK showed significantly higher levels of interspecific species delimitation than rbcL and trnH-psbA. A combination of matK and ITS was the most efficient DNA barcode among all studied regions, however, they do not represent an appropriate candidate barcode for Chinese Gaultheria, by which only 11 out of 30 species can be separated. Loci rbcL, matK, and trnH-psbA, which were recently proposed as universal plant barcodes, have a very poor capacity for species separation for Chinese Gaultheria. DNA barcodes may be reliable tools to identify the evolutionary units of this group, so further studies are needed to develop more efficient DNA barcodes for Gaultheria and other genera with complicated evolutionary histories.

One application of DNA barcoding is species identification based on sequences of a short and standardized DNA region. In plants, various DNA regions, alone or in combination, have been proposed and investigated, but consensus on a universal plant barcode remains elusive. In this study, we tested the utility of four candidate barcoding regions (rbcL, matK, trnH-psbA, and internal transcribed spacer (ITS)) as DNA barcodes for discriminating species in a large and hemiparasitic genus Pedicularis (Orobanchaceae). Amplification and sequencing was successful using single primer pairs for rbcL, trnH-psbA, and ITS, whereas two primer pairs were required for matK. Patterns of sequence divergence commonly showed a “barcoding gap”, that is, a bimodal frequency distribution of pairwise distances representing genetic diversity within and between species, respectively. Considering primer universality, ease of amplification and sequencing, and performance in discriminating species, we found the most effective single-region barcode for Pedicularis to be ITS, and the most effective two-region barcode to be rbcL + ITS. Both discriminated at least 78% of the 88 species and correctly identified at least 89% of the sequences in our sample, and were effective in placing unidentified samples in known species groups. Our results suggest that DNA barcoding has the potential to aid taxonomic research in Pedicularis, a species-rich cosmopolitan clade much in need of revision, as well as ecological studies in its center of diversity, the Hengduan Mountains region of China.

The difficulty in clarifying species of genus Ligularia Cass. has been attributed to rapid and continuous allopatric speciation in small and isolated populations, combined with interspecific diploid hybridization in the Qinghai-Tibetan Plateau and adjacent areas. However, no concrete example has been reported to prove this hypothesis. We studied a natural mixed population of six species of Ligularia in which some individuals were morphologically intermediate between L. subspicata and L. nelumbifolia. Based on DNA sequences (trnC-F, trnL-rpL32, trnQ-5′rps16, trnK-rps16, and internal transcribed spacer) and inter-simple sequence repeat data, we concluded that putative hybrids are primarily products of hybridization between L. nelumbifolia and L. subspicata. The other four species or additional, unknown species may also be involved in hybridization. This hybridization is bidirectional but asymmetrical. Hybrid individuals were mostly the first generation, but F₂ and later-generation hybrids were also present. Moreover, the backcrossed individuals detected indicate that natural gene flow occurs among at least three Ligularia species. Hybrids may become stabilized to form new species or may function as intermediates in evolutionary diversification.

A natural hybrid species in Petrocosmea named Longianthera in Yanshan County, Yunnan Province is confirmed for the first time based on molecular and morphological evidence. The character count procedure of the variable characters show that Longianthera populations are characteristic of the intermediate morphological traits between its putative parents Yanshan and Petrocosmea martinii. The nuclear ribosomal internal transcribed spacer region and three chloroplast regions of matK, trnL-F, and trnT-L are sequenced in the putative hybrid and the related species. Both alignment of DNA sequences and the phylogenetic trees could exclude all the other species in Petrocosmea as the parental species except for Yanshan and P. martinii. Eight haplotypes in the 31 internal transcribed spacer sequences and six haplotypes in 42 cpDNA sequences were found from 14 individuals of Longianthera populations. The analyses of DNA sequences, haplotypes, and phylogenetic trees indicate that Longianthera is likely a hybrid species between its putative parents Yanshan and P. martinii, in which Yanshan might be the most possible maternal parent. Several factors may contribute to the natural hybridization between these two parental species in Petrocosmea, such as the overlapped geographic distribution, habitats, flowering periods, and shared pollinators. Finally, the new species of Yanshan and the natural hybrid species of Longianthera are described.

Paeonia decomposita Hand.-Mazz. subsp. rotundiloba D. Y. Hong is here raised to the specific rank, P. rotundiloba (D. Y. Hong) D. Y. Hong, based on its distinctiveness of four diagnostic characters: number of carpels; height of disk; number of leaflets of the lower leaves, and shape of the terminal leaflets; and unpublished molecular data. Paeonia rotundiloba differs distinctly from P. decomposita in having carpels mostly 3, less often 2 or 4, very rarely 5 (vs. almost always 5, very occasionally 4 or 3), disk 8–15 mm high (vs. 4–9.6 mm), leaflets mostly 19–39 (vs. 29–63) in number, and ratio of length to width of the terminal leaflets 1.09–1.93 (vs. 1.81–2.99).

Piper protrusum Chaveer. & Tanee, sp. nov. is described and illustrated. It dominantly comprises three branching types with three different types of leaf blades, bases, and apexes. The critical distinguishing character is the protruded receptacle having a bract and nine stamens. Individual plants have been discovered in areas of Southern Thailand since 2004 without reproductive parts. The investigated sites were revisited several times, and an individual with flowers was finally found in July 2009. Phylogenetic analysis of the new species and five similar species is carried out based on DNA fingerprinting. The genetic distances between the new species and five similar species range from 0.25 to 0.35, supporting new species designation. Molecular data conform to morphological data in validating that it is a new species. Additionally, its DNA barcodes have been provided for further identification in case the morphological data is unclear. The sequence data have been submitted to the GenBank database under accession numbers GU980898 (rpoB gene), GU980899 (rpoC1 gene), and GU980900 (psbA-trnH region).

A freshwater dinoflagellate was identified as Durinskia baltica (Levander) Carty & Cox by morphological characteristics, with the plate formula: Po, x, 4′, 2a, 6″, 5c, 4s, 5‴, 2″″. Durinskia was a newly recorded dinoflagellate genus for China with two anterior intercalary plates and six characteristic precingular plates. Partial sequences of the small and large subunit ribosomal DNA and internal transcribed spacer sequences for the dinoflagellate cells were obtained from field samples. Molecular phylogenetic results indicated Durinskia species could cluster into a monophyletic group, which were distinct from Peridinium species. According to morphological and molecular evidence, it was agreed that the genus Durinskia was separated from the genus Peridinium, which could be a polyphyletic group. In addition, D. baltica was an infrequent diatom-harboring dinoflagellate which was known to possess an endosymbiotic diatom or diatom-like alga. The phylogenetic analyses indicated that D. baltica had a close affinity with Peridiniopsis penardii and P. niei, common freshwater bloom-forming species in China.

A population of Meridion circulare var. circulare (Greville) C.A. Agardh from Inner Mongolia was found to produce Innenschalen or internal spores. Examination of this population with light and scanning electron microscopy showed morphological differentiation between vegetative and spore morphologies. Vegetative valves typically bear costae and one rimoportula at the headpole. Spores lack costae and have two rimoportulae, one at the headpole and the other at the footpole. There is plasticity in the production of valve morphologies, and a variety of vegetative valve and spore combinations are evident. This population of M. circulare var. circulare has initial valves of over 90 μm in length, and all of the initial cells encountered are acostate and bear two rimoportulae. These observations suggest that either spores are the product of sexual reproduction, or that initial valves may be produced parthenogenetically in Meridion. Spores as products of the sexual process have not been reported in diatoms previously, and parthenogenesis in Meridion was reported previously but discounted in other published reports. The plasticity of valve morphologies expressed in M. circulare var. ciculare, between vegetative valves and spores (and back) across a short temporal period suggests that diatoms can alter their cell wall structure dramatically and quickly in response to external variables.

Principal component analysis of specimen measurements revealed morphological variation within Chinese Calamagrostis epigeios correlated with differences in geographical distribution. We conducted a morphological examination of specimens from the range of the species, with the goal of developing a treatment for its Chinese members reflecting the global diversity complex. The confusing taxonomy of this complex is clarified with the recognition of three species in China, namely C. epigeios, C. extremiorientalis, and C. macrolepis. Calamagrostis epigeios is an exclusively temperate grass occurring in the northwestern, northern, and northeastern parts of China. It has spikelets 4–7 mm long, glumes equal or subequal, awn arising near the middle of the lemma back, upper leaf surface smooth and with shallow ribs and furrows. Calamagrostis extremiorientalis is a tropical and subtropical grass that occurs in the southwest provinces of China (except Xizang) throughout south central provinces and east to the northeastern parts of China. It is morphologically similar to C. epigeios. However, C. extremiorientalis has the awn arising from the upper one-third of the lemma back, upper leaf surface scabrid because of the presence of short stiff hairs, and with tall ribs and deep furrows. Calamagrostis macrolepis occurs in the northwestern, northern, and northeastern parts of China. It has a robust habit, spikelets 6.5–11 mm long, and glumes unequal, the upper 1–1.5 mm shorter than the lower. New synonyms, descriptions, and citations of representative specimens are provided for each species, along with an identification key.