Progress report on the study of wood-decaying fungi in China

This study addressed three important aims:(1) undermining the previously obtained raw data about wood-decaying fungi(WDF) distribution and continuously investigating permanent plots to address certain scientific questions in ecology,(2) resolving the higher-level phylogeny of WDF with the help of multiple loci,and(3) testing and estimating the medicinal values of species that are closely related to well-known medicinal species.More than 1200 species and 2469 strains of WDF in China were identified from 28908 specimens collected from a series of field investigations.Using these materials,studies in multiple disciplines,such as ecology,taxonomy and phylogeny,and medicine,have been performed.With respect to ecology,the diversity of wood-decaying polypores significantly differed among a boreal forest zone,a temperate and warm temperate forest zone,and a tropical and subtropical forest zone.For instance,from north to south,the number and proportion of brown-rot species and the proportion of species found on fallen trunks were both decreased.The ecological patterns of wood-decaying polypores on gymnosperm and angiosperm trees were also explored by a case study in Northeast China.Although the total species richness was similar between the two tree groups,several other characteristics were significantly different,such as community structure and richness in certain substrates.The taxonomy and phylogeny of wide samples were referred to and their phylogenetic positions were resolved or at least partially established.In particular,phylogenetic knowledge about four genera,Fomitiporia,Ganoderma,Inonotus and Perenniporia,which include medicinal species,was essential for further research to determine the medicinal values of these types of fungi.Among these medicinal species,we mainly focused on Inonotus obliquus for its medicinal purposes.Polyphenols,polysaccharides and lanostane-type triterpenoids,extracted from the sterile conk of this species,could dramatically decrease levels of free radicals,DPPH and hydroxyl radicals,respectively.The metabolic profiles(both production and composition) of cultured I.obliquus mycelia could be altered by co-culture with other medicinal species or by induction of S-nitrosylation and denitrosylation,which may enhance the antioxidant capacity of I.obliquus.     

Molecular phylogeny of European and African Barbus and their West Asian relatives in the Cyprininae (Teleostei: Cypriniformes) and orogenesis of the Qinghai-Tibetan Plateau

The phylogenetic relationships of European and African Barbus and their West Asian relatives in Cyprininae remain largely unresolved. Consequently, little is known about the drivers of their evolution, including the possible association of uplifting of the Qinghai-Tibetan Plateau (QTP) with the early divergence of the subfamily. We use complete sequence data of the mitochondrial DNA gene encoding the protein cytochrome b (Cytb) to hypothesize the phylogeny of 85 species belonging to 47 genera in the Cyprininae plus 6 species from the Leuciscinae. We employ 6 other species from Cypriniformes as outgroup taxa and estimate divergence times. Our results indicate that European Barbus sensu stricto lineage including Aulopyge shares a common ancestor with specialized and highly specialized schizothoracins and the genera Cyprinion and Scaphiodonichtys. The common ancestor appears to have originated in the Qinghai-Tibetan Plateau (QTP) region about 19.4–17.8 Ma. Barbus sensu stricto lineage appears to have originated about 16.6–15.5 Ma. Small to medium sized African Barbus sensu lato appear to have had an Oriental origin about 19.1–15.3 Ma and are closely related to Asian Puntius. West Asian Carasobarbus lineage including large African Barbus sensu lato might have originated about 9.94 Ma, also in Oriental Realm and has a close relationship to Asian Neolissochilus and Tor. The large-sized Barbus sensu lato appear to have diverged from Carasobarbus about 7.7 Ma. Finally, the Cyprininae appear to have radiated rapidly into nine lineages and many sublineages from about 27.8 to 17.8 Ma, close to the time of the second-stage tectonic movements of the QTP. Our analyses provide evidence that the uplifting of the QTP drove early diversification of the Cyprininae. Our extensive sampling of species involving all of the important areas results in clear evolutionary scenario for the Cyprininae.     

Phylogenetic investigation on five genera of tintinnid ciliates （Ciliophora, Choreotrichia）, based on the small subunit ribosomal RNA gene sequences

The phylogenetic relationship among tintinnid ciliates are relatively poorly studied based on molecular data. In the present work, seven species belonging to five genera of the order Tintinnida (Amphorellopsis acuta, Codonellopsis nipponica, Favella taraikaensis, Stenosemella nivalis, Tintinnopsis beroidea, Tintinnopsis cylindrica and Tintinnopsis lohmanni) were analyzed using the information on their small subunit ribosomal RNA gene sequences. Phylogenetic trees were constructed using Bayesian inference (BI), maximum parsimony (MP), neighbor-joining (NJ), and least-squares (LS) methods. Generally, similar topologies were revealed with high or moderate supports, in which the main results show that (1) all tintinnids analyzed belong to a single assemblage; (2) congeners in Tintinnopsis do not cluster together, which indicates that the lorica-based definition for this genus is not consistent with the SSU rRNA phylogeny; (3) A. acuta groups with Tintinnidium mucicola but not with Eutintinnus, indicating that the traditional family Tintinnidae might be a paraphyletic group; (4) Stenosemella and Codonellopsis are clearly most related and possibly even merged into one genus regarding their similar morphology and molecular analyses, and possession of a hyaline collar is the only characteristic of the genus.     

Analysis of diversity of CO I gene and system generation of nine species of chitons

Cytochrome c oxidase subunit Ⅰ(COⅠ) genes from 9 chiton species in China’s coast area were sequenced. A phylogeny tree about these gene sequences were reconstructed together with other 4 COⅠgene sequences of chitons from Genbank. The affinity genetic relationship and the taxonomic status of molecular evolution for these 13 chiton species were analyzed. The results show that Liolophura japonica and Onithochiton hirasei belong to Chitonidae, Acanthochiton rubrolineatus and Acanthochiton dissimilis belong to Acanthochitonidae, and Placiphorella japonica and Mopalia retifera belong to the same family Mopliidae. However, Lepidozona coreanica, Ischnochiton comptus, and Ischnochiton hakodadensis are not supposed to be referred to Ischnochi-tonidae according to the genetic distance analysis (L. coreanica, I. comptus, and I. hakodadensis are usually classed as Ischnochitonidae according to their morphological character). Furthermore, I. hakodadensis could not been classed as Ischnochiton, and it is more likely to be treated as a close relative of Lepidozona.     

Chemical and biological research of Clematis medicinal resources

Clematis is a botanical source for various pharmaceutically active components,which has long been used in conventional medicine since the beginning of Chinese civilization.Increasing interest in Clematis medicinal resources has led to additional discoveries of triterpenoid saponins,flavonoids,coumarins,alkaloids and many other compounds in various Clematis species,and to investigations on their chemotaxonomy,molecular phylogeny and pharmacology.In continuation with our studies on Clematis chemistry and biology,we review the chemistry,chemotaxonomy,molecular biology and phylogeny of Clematis and their relevance to drug efficacy and drug development.Various databases and technology have been used in literature search in order to characterize the global scientific effort.It is essential to study more species for both the sustainable utilization of Clematis medicinal resources and finding novel compounds with potential clinical utility.Systems biology and omics technologies will play an increasingly important role in future medicinal research involving bioactive compounds of Clematis.     

Fungal genus Hypocrea/Trichoderma: from barcodes to biodiversity

Hypocrea/Trichoderma is a genus of soil-borne or wood-decaying fungi containing members important to mankind as producers of industrial enzymes and biocontrol agents against plant pathogens, but also as opportunistic pathogens of immunocompromised humans and animals, while others can cause damage to cultivated mushroom. With the recent advent of a reliable, BarCode-aided identification system for all known taxa of Trichoderma and Hypocrea, it became now possible to study some of the biological fundamentals of the diversity in this fungal genus in more detail. In this article, we will therefore review recent progress in （1） the understanding of the geographic distribution of individual taxa; （2） mechanisms of speciation leading to development of mushroom diseases and facultative human mycoses; and （3） the possible correlation of specific traits of secondary metabolism and molecular phylogeny.     

Molecular identification and phylosenetic position of Cuora yunnanensis

The Yunnan box turtle （Cuora yunnanensis, Boulenger, 1906）, which has drawn much attention in conservation biology, was regarded as extinct since it was previously known only from 12 specimens collected in Yunnan, China, before 1908. Recently, live specimens have been discovered which are suggested to be C. yunnanensis. To determine whether the newly discovered specimens are really C. yunnanensis, we have established a molecular phylogeny, with a 1725-bp fragment of mitochondrial DNA, using samples from three live individuals of C. yunnanensis, together with sequence data from a museum specimen of C. yunnanensis （MNHN 1907.10） and other members of the genus Cuora. We found that the three newly discovered individuals and the old museum specimen of C. yunnanensis are very similar both in morphology and in mitochondrial DNA sequence, suggesting that the three new individuals are the very C. yunnanensis, and thus the species is not extinct. Our phylogenetic analysis also demonstrates that C. yunnanensis is not of recent hybrid origin, but rather represents a distinct evolutionary lineage.     

Taxonomic relationship betweenOryza minuta andO. officinalis based on AP-PCR analysis

The arbitrarily primed polymerase chain reaction (AP-PCR) technique was used to detect polymorphisms in genomic DNA fromOryza minuta, O. officinalis, and related rice species. The results show that the genetic distance betweenO. minuta andO. officinalis is much higher than that between two known species,O. sativa andO. rufipogon, showing thatO. minuta andO. officinalis should be classified as two different species in genusOryza, and that the AP-PCR technique can be used as a powerful tool for studying taxonomic relationships among related species, and even subspecies. Supported by the National Natural Science Foundation of China Yi Qingming: born in Apr. 1938, Professor     

First discovery of fossil Diplothrix (Muridae, Rodentia) outside the Ryukyu Islands, Japan

The first Diplothrix (Muridae, Rodentia) fossils of the early Early Pleistocene are described as D. yangziensis sp. nov., which were collected from the Renzidong Cave deposits in Anhui Province, Eastern China. Diplothrix was previously represented by a single species, D. legata, whose geographical distribution during the Late Pleistocene is restricted to the Ryukyu Islands, Japan. With straight chevrons on M1, distinct t3 and t9 on upper molars, primitive M3, mlc on m1, and developed a-lab on m2 and m3, the new species is morphologically distinct from other large murids in East Asia, and should belong to the genus Diplothrix. There are also differences in molar morphology between the new species and D. legata, the type species of Diplothrix, as well as other known fossils. For example, D. yangziensis sp. nov. has a smaller size, a more elongated crown, developed precingulum and pc on M1, more primitive M3, weaker mlc and more primitive pc on m1, and stronger plc and pc on m3. In short, Diplothrix yangziensis sp. nov. is evidently more primitive than D. legata, suggesting that the former is likely the ancestor of the latter. Diplothrix yangziensis sp. nov. is the first discovery of the genus outside the Ryukyu Islands, Japan and is also the earliest and most primitive species of the genus in Eurasia. Its discovery has significant implications for reconstructing the evolution and dispersal pattern of Diplothrix, as well as for discussing its palaeoecological variation.     

Synchronous drying and cooling in central Asia during late Oligocene

Aridification of central Asia during late Oligocene and Early Miocene has been documented by numerous eolian records from the North Pacific and central Asia. However, direct evidence of aridity from the interior of the arid zone is still rather scarce. To better reconstruct the climate history in central Asia during the late Oligocene, we have analyzed ostracod assemblages and gypsum content in the sediments from the lacustrine Jingou River section in the northern Tianshan Mountains. Our results show that the cold water species Candona cf. Neglecta and Pseudocandona albicans replaced the warm water species Ilyocypris bradyi and Ilyocypris sp. to become the dominant species at 23.8 Ma, indicating significant cooling in central Asia at that time. At the same time, a substantial increase in gypsum content indicates the intensification of central Asian drying. The synchronous cooling and drying approximately coincided with the Oi2b.1 and/or Mi1 events, implying a causal linkage between late Oligocene global cooling and central Asian aridity.     

The yellow sea green tides were dominated by one species, Ulva (Enteromorpha) prolifera, from 2007 to 2011

Green tides have occurred in the Yellow Sea successively from 2007 to 2011. Genetic analysis of the 5-year green-tide-forming algae needs to be performed to determine the source of the biomass and understand the mechanism of the green tide blooms. In this study, free-floating green algae were collected at different sites in the Yellow Sea in 2010 and 2011. Data on 182 free-floating samples and 155 attached Ulva samples from previous studies on the Yellow Sea green tides from 2007 to 2009 were also taken into consideration. Morphology observation and molecular phylogenetic analyses indicated that the Yellow Sea green tides were dominated by a single species, Ulva prolifera, from 2007 to 2011. Considering that at least five Ulva species inhabit the north coast of China, the unialgal composition of the green tides implied that (1) there may be some special physiology and propagation pathways of U. prolifera for its rapid expansion, (2) the mechanisms of the Yellow Sea green tide formation were similar for the last five years, and (3) the intra-species genetic variation and population structure of U. prolifera need to be studied to determine the exact origin of the bloom-forming biomass.     

Different responses of two Mosla species to potassium limitation in relation to acid rain deposition

The increasingly serious problem of acid rain is leading to increased potassium (K) loss from soils, and in our field investigation, we found that even congenerically relative Mosla species show different tolerance to K-deficiency. A hydroponic study was conducted on the growth of two Mosla species and their morphological, physiological and stoichiometric traits in response to limited (0.35 mmol K/L), normal (3.25 mmol K/L) and excessive (6.50 mmol K/L) K concentrations. Mosla hangchowensis is an endangered plant, whereas Mosla dianthera a widespread weed. In the case of M. hangchowensis, in comparison with normal K concentration, K-limitation induced a significant reduction in net photosynthetic rate (P _n), soluble protein content, and superoxide dismutase (SOD) activity, but an increase in malondialdehyde (MDA) concentration. However, leaf mass ratio (LMR) and root mass ratio (RMR) were changed little by K-limitation. In contrast, for M. dianthera, K-limitation had little effect on P _n, soluble protein content, SOD activity, and MDA concentration, but increased LMR and RMR. Critical values of N (nitrogen):K and K:P (phosphorus) ratios in the shoots indicated that limitation in acquiring K occurred under K-limited conditions for M. hangchowensis but not for M. dianthera. We found that low K content in natural habitats was a restrictive factor in the growth and distribution of M. hangchowensis, and soil K-deficiency caused by acid rain worsened the situation of M. hangchowensis, while M. dianthera could well acclimate to the increasing K-deficiency. We suggest that controlling the acid rain and applying K fertilizers may be an effective way to rescue the endangered M. hangchowensis.     

A simple and effective method for total RNA isolation of appressoria in Magnaporthe oryzae

Appressorium formation is an important event in establishing a successful interaction between the rice blast fungus, Magnaporthe oryzae, and its host plant, rice. An understanding of molecular events occurring in appressorium differentiation will give new strategies to control rice blast. A quick and reliable method to extract total RNA from appressorium is essential for studying gene expression during appressorium formation and its mechanism. We found that duplicate film is an efficient substratum for appressorium formation, even when inoculated with high density conidia. When inoculated with conidia at 1 × 106 ml^-1, the percentages of conidium germination and appressorium formation were （97.98±0.67）% and （97.88±0.45）%, respectively. We applied Trizol before appressorium collection for total RNA isolation, and as much as 113.6 lag total RNA was isolated from the mature appressoria at 24 h after inoculation. Functional analysis of two genes, MNH6 and MgATG1, isolated from the cDNA subtractive library, revealed that the quantity of RNA was good enough to construct a cDNA （complementary DNA） library or a cDNA subtractive library. This method may be also applicable for the appressorium RNA isolation of other pathogenic fungi in which conidia differentiate into appressoria in the early stages of host infection.     

A wound-induced small polypeptide gene family is upregulated in soybean nodules

Small peptides function as key signals in processes, such as plant cell differentiation, organ development and defenses to biotic stresses. A large number of small peptide precursor genes have been predicted from the analysis of the soybean (Glycine max) whole genome DNA sequence. However, most of these genes have unknown characteristics and functions. In this report, we systemically searched for the gene families of small peptide precursors that are up-regulated in soybean nitrogen-fixing root nodules. We found 212 genes (encoding peptides shorter than 150 amino acids) that were up-regulated, and among them, 79 genes belong to 38 multiple-gene families, but the other 133 genes are unique. Twenty-eight of 38 families are conserved in Arabidopsis, but the other 10 only exist in legumes. We also identified 16 out of the 38 members of the wound-induced polypeptide (WIP) gene family to be upregulated in nitrogen-fixing nodules. We further analyzed homologs of WIP genes in Medicago, Lotus, Arabidopsis and Oryza species and found that a few homologous genes from Medicago truncatula and Lotus japonicus were also upregulated in their nodules and some WIP genes were induced by specific fungal pathogens on soybean and rice. Structure prediction indicated that all WIP prepropeptides contain a conserved DUF3774 domain (including two hydrophobic regions) and most of them have an N-terminal signal sequence. Fluorescence microscopy analysis of two WIP prepropeptides fused to GFP revealed that these proteins are located on the plasma membrane of tobacco leaf cells. Interestingly, 34 soybean WIP genes are clustered onto three soybean chromosomes, different from known peptide gene families (such as CLE). Among them, 11 highly identical genes are aligned on the 6th chromosome, 12 on the 12th, and 11 on the 13th chromosomes. Most of WIP genes from the 12th chromosome share the highest identities with their homologs on the 13th chromosome, suggesting that ancestral WIP genes could have originated from the 13th chromosome, then spread onto the 12th chromosome by chromosome homologous recombination; the new WIP genes could have existed in multiple copies by gene duplication which then spread onto the 6th chromosome. In Arabidopsis and Oryza species, half of the WIP genes are also aligned on one chromosome and showed higher identity with those from the soybean 12th and 13th chromosomes, suggesting that WIP genes originated from one common ancestor.     

Mitochondrial 16S rRNA sequence variations and phylogeny of the Chinese sisorid catfishes

Partial sequences of mitochondrial 16S rRNA gene were obtained by PCR amplification for comparisons among nine species of glyptosternoid fishes and six species of non-glyptosternoids representing 10 sisorid genera. There are compositional biases in the A-rich unpaired regions and G-rich paired regions. A-G transitions are primarily responsible for the Ts/Tv bias in unpaired regions. The overall substitution rate in unpaired regions is almost two times higher than that in the paired regions. Saturation plots at comparable levels of sequence divergence demonstrate no saturation effects. Phylogenetic analyses using both maximum likelihood and Bayesian methods support the monophyly of Sisoridae. Chinese sisorid catfishes are composed of two majorlineages, one represented by (Gagata (Bagarius, Glyptothorax)) and the other by “glyptosternoids Pseudecheneis“. The glyptosternoids may not be a monophyletic group. A previous hypothesis referring to Pseudecheneis as the sister group of monophyletic glyptosternoids, based on morphological evidence, is not supported by the molecular data. Pseudecheneis is shown to be a sister taxon of Glaridoglanis. Pareuchiloglanis might be paraphyletic with Pseudexostoma and Euchiloglanis. Our results also support the hypothesis that Pareuchiloglanis anteanalis might be considered as the synonyms of Pareuchiloglanis sinensis, and genus Euchiloglanis might have only one valid species, Euchiloglanis davidi.     

Fungal diversity on fallen leaves of Ficus in northern Thailand

Fallen leaves of Ficus altissima, F. virens, F. benjamina, F. fistulosa and F. semicordata, were collected in Chiang Mai Province in northern Thailand and examined for fungi. Eighty taxa were identified, comprising 56 anamorphic taxa, 23 ascomycetes and l basidiomycete. Common fungal species occurring on five host species with high frequency of occurrence were Beltraniella nilgirica, Lasiodiplodia theobromae, Ophioceras leptosporum, Periconia byssoides and Septonema harknessi. Colletotrichum and Stachybotrys were also common genera. The leaves of different Ficus species supported diverse fungal taxa, and the fungal assemblages on the different hosts showed varying overlap. The fungal diversity of saprobes at the host species level is discussed.     

基于Cyt b基因全序列分析河南7种菊头蝠系统发育关系

采用分子系统发育分析方法对菊头蝠科蝙蝠的系统发育关系和分类地位进行研究,以7种127个蝙蝠为研究对象,测定了mtDNA Cytb基因全序列(1140kb),用最大简约法(maximum parsimony,MP)和最大似然法(maximum likelihood,ML)建系统发育树,对菊头蝠种间亲缘关系及分类地位进行分析,角菊头蝠、菲菊头蝠和大耳菊头蝠属于较原始的种类,且彼此间有较近的亲缘关系;大菊头蝠、皮氏菊头蝠关系较近,为较原始的类群;马铁和中菊头蝠关系较近,为后分化的类群.     

Evolution of stomatal and trichome density of the Quercus delavayi complex since the late Miocene

A fossil oak species,Quercus tenuipilosa Q.Hu et Z.K.Zhou,is reported from the upper Pliocene Ciying Formation in Kunming,Yunnan Province,southwestern China.The establishment of this species is based on detailed morphologic and cuticular investigations.The fossil leaves are elliptic,with serrate margins on the apical half.The primary venation is pinnate,and the major secondary venation is craspedodromous.The tertiary veins are opposite or alternate-opposite percurrent with two branches.The stomata are anomocytic,occurring only on the abaxial epidermis.The trichome bases are unicellular or multicellular.The new fossil species shows the closest affinity with theextant Q.delavayi and the late Miocene Q.praedelavayi Y.W.Xing et Z.K.Zhou from the Xiaolongtan Formation of the Yunnan Province.All three species share similar leaf morphology,but differ with respect to trichome base and stomatal densities.Q.tenuipilosa.Q.praedelavayi,and Q.delavayi can be considered to constitute the Q.delavayi complex.Since the late Miocene,a gradual reduction in trichome base density has occurred in this complex.This trend is the opposite of that of precipitation,indicating that increased trichome density is not an adaptation to dry environments.The stomatal density(SD)of the Q.delavayi complex was the highest during the late Miocene,declined in the late Pliocene,and then increased during the present epoch.These values show an inverse relationship with atmospheric CO_2 concentrations,suggesting that the SD of the Q.delavayi complex may be a useful proxy for reconstruction of paleo-CO_2 concentrations.     

Noeggerathiales as coal-forming plants in Cathaysia: conclusions from an Early Permian vegetational Pompeii in Inner Mongolia

Noeggerathiales are an extinct group of sporebearing plants of uncertain systematic position that are known from Carboniferous and Permian age Euramerican and Cathaysian floras that occurred in presentday Europe, North America, and East Asia. The order Noeggerathiales includes over 50 species of more than 20 fossil genera, but their paleoecology is not well understood yet. Previously this group had been found only in extrabasinal floras or those inhabiting clastic wetlands. Noeggerathiales have never been recorded in coal ball floras. Thus, it is up to now uncertain whether this group has contributed to the formation of coal. Recent investigations of an Early Permian peatforming flora of the Taiyuan Formation near Wuda, Inner Mongolia, which was preserved in a volcanic ash fall has provided evidence that noeggerathialean plants not only existed in the peatforming vegetation but could even be the dominant group in some areas of the coal swamp. The Noeggerathiales in this particular peatforming forest include Tingia unita, Paratingia wudensis, and a new species of Paratingia. Exceptionally well-preserved specimens indicate that these noeggerathialean plants are small trees with a canopy of compound leaves and strobili near the top of an unbranched （monocaulous） stem.