Guizhou Academy of Agricultural science
Guizhou Academy of Agricultural science
Liu J.-K.,CAS Kunming Institute of Botany |
Liu J.-K.,Guizhou Academy of Agricultural science |
Hyde K.D.,Mae Fah Luang University |
Jeewon R.,University of Mauritius |
And 5 more authors.
Fungal Diversity | Year: 2017
The current classification system for the recognition of taxonomic ranks among fungi, especially at high-ranking level, is subjective. With the development of molecular approaches and the availability of fossil calibration data, the use of divergence times as a universally standardized criterion for ranking taxa has now become possible. We can therefore date the origin of Ascomycota lineages by using molecular clock methods and establish the divergence times for the orders and families of Dothideomycetes. We chose Dothideomycetes, the largest class of the phylum Ascomycota, which contains 32 orders, to establish ages at which points orders have split; and Pleosporales, the largest order of Dothideomycetes with 55 families, to establish family divergence times. We have assembled a multi-gene data set (LSU, SSU, TEF1 and RPB2) from 391 taxa representing most family groups of Dothideomycetes and utilized fossil calibration points solely from within the ascomycetes and a Bayesian approach to establish divergence times of Dothideomycetes lineages. Two separated datasets were analysed: (i) 272 taxa representing 32 orders of Dothideomycetes were included for the order level analysis, and (ii) 191 taxa representing 55 families of Pleosporales were included for the family level analysis. Our results indicate that divergence times (crown age) for most orders (20 out of 32, or 63%) are between 100 and 220 Mya, while divergence times for most families (39 out of 55, or 71%) are between 20 and 100 Mya. We believe that divergence times can provide additional evidence to support establishment of higher level taxa, such as families, orders and classes. Taking advantage of this added approach, we can strive towards establishing a standardized taxonomic system both within and outside Fungi. In this study we found that molecular dating coupled with phylogenetic inferences provides no support for the taxonomic status of two currently recognized orders, namely Bezerromycetales and Wiesneriomycetales and these are treated as synonyms of Tubeufiales while Asterotexiales is treated as a synonym of Asterinales. In addition, we provide an updated phylogenetic assessment of Dothideomycetes previously published as the Families of Dothideomycetes in 2013 with a further ten orders and 35 families. © 2017, School of Science.
Latrasse D.,8618 UniversiteParis Sud |
Jegu T.,8618 UniversiteParis Sud |
Meng P.-H.,8618 UniversiteParis Sud |
Meng P.-H.,Guizhou Academy of Agricultural science |
And 9 more authors.
Nucleic Acids Research | Year: 2013
Because regulation of its activity is instrumental either to support cell proliferation and growth or to promote cell death, the universal myo-inositol phosphate synthase (MIPS), responsible for myo-inositol biosynthesis, is a critical enzyme of primary metabolism. Surprisingly, we found this enzyme to be imported in the nucleus and to interact with the histone methyltransferases ATXR5 and ATXR6, raising the question of whether MIPS1 has a function in transcriptional regulation. Here, we demonstrate that MIPS1 binds directly to its promoter to stimulate its own expression by locally inhibiting the spreading of ATXR5/6-dependent heterochromatin marks coming from a transposable element. Furthermore, on activation of pathogen response, MIPS1 expression is reduced epigenetically, providing evidence for a complex regulatory mechanism acting at the transcriptional level. Thus, in plants, MIPS1 appears to have evolved as a protein that connects cellular metabolism, pathogen response and chromatin remodeling. © The Author(s) 2013.
Yang Y.,Guizhou Academy of Agricultural science |
Yang Y.,Liupanshui Normal College |
Cal L.,CAS Institute of Microbiology |
Yu Z.,Huazhong Agricultural University |
And 3 more authors.
Cryptogamie, Mycologie | Year: 2011
Twenty-two strains of Colletotrichum, representing eight species, were isolated from eight genera of Orchidaceae in Yunnan and Guizhou provinces in China. Fourteen strains were from lesions and are pathogens, four were from fallen/dead flowers or stems and four were isolated as endophytes. The strains are characterized through morphological studies and multilocus phylogenetic analysis (ACT, Tub 2, CAL, CHS I, GPDH and ITS). Colletotrichum orchidearum and the new species Colletotrichum karstii are described and illustrated, based on morphological characters and multilocus sequence data. Collections of the other Colletotrichum species are reported with notes. © 2011 Adac. Tous droits r6serv6s.
Zhang L.,CAS Institute of Genetics and Developmental Biology |
Zhang L.,Guizhou Academy of Agricultural science |
Liu D.,CAS Institute of Genetics and Developmental Biology |
Guo X.,China Agricultural University |
And 5 more authors.
BMC Genetics | Year: 2011
Background: In order to help establish heterotic groups of Chinese northern wheat cultivars (lines), Diversity arrays technology (DArT) markers were used to investigate the genetic diversity and population structure of Chinese common wheat (Triticum aestivum L.).Results: In total, 1637 of 7000 DArT markers were polymorphic and scored with high confidence among a collection of 111 lines composed mostly of cultivars and breeding lines from northern China. The polymorphism information content (PIC) of DArT markers ranged from 0.03 to 0.50, with an average of 0.40, with P > 80 (reliable markers). With principal-coordinates analysis (PCoA) of DArT data either from the whole genome or from the B-genome alone, all lines fell into one of two major groups reflecting 1RS/1BL type (1RS/1BL and non-1RS/1BL). Evidence of geographic clustering of genotypes was also observed using DArT markers from the A genome. Cluster analysis based on the unweighted pair-group method with algorithmic mean suggested the existence of two subgroups within the non-1RS/1BL group and four subgroups within the 1RS/1BL group. Furthermore, analysis of molecular variance (AMOVA) revealed highly significant (P < 0.001) genetic variance within and among subgroups and among groups.Conclusion: These results provide valuable information for selecting crossing parents and establishing heterotic groups in the Chinese wheat-breeding program. © 2011 Zhang et al; licensee BioMed Central Ltd.
Peng L.,Guizhou University |
Yang Y.,Liupanshui Teachers College |
Hyde K.D.,Mae Fah Luang University |
Bahkali A.H.,King Saud University |
And 2 more authors.
Cryptogamie, Mycologie | Year: 2012
Thirty-eight strains of Colletotrichum were isolated from diseased Citrus leaves in Guizhou and Yunnan provinces in China. Based on morphological characters and multilocus sequence data, the strains were identified as C. boninense (1 strain), C. brevispora (1), C. fructicola (2), C. gloeosporioides (29), C. karstii (2), C. simmondsii (1) and Colletotrichum murrayae; the latter represents a new species which is described in this paper. Colletotrichum gloeosporioides was originally isolated from Citrus sinensis in southern Italy and was the most common species associated with diseased leaves of Citrus in China. © 2012 Adac. Tous droits réservés.
Thambugala K.M.,Guizhou Academy of Agricultural science |
Thambugala K.M.,Mae Fah Luang University |
Ariyawansa H.A.,Mae Fah Luang University |
Liu Z.-Y.,Guizhou Academy of Agricultural science |
And 2 more authors.
Phytotaxa | Year: 2014
The type specimens of Dolabra, Placostromella, Pleosphaerellula, Polysporidiella and Pseudotrichia were re-examined in order to suggest their familial and higher placement according to the morphology based on modern taxonomic concepts. An overview of the history and descriptions and illustrations of these genera are provided. Based on morphological similarities, Placostromella is placed in Parmulariaceae, while Pseudotrichia is transferred to Montagnulaceae. Pleosphaerellula is placed in Pleosporales, genera incertae sedis and Polysporidiella is retained in Dothideomycetes, genera incertae sedis as it is not typical of any existing family of Dothideomycetes. According to published phylogenetic data, Dolabra belongs in Chaetothyriomycetidae, genera incertae sedis (Eurotiomycetes). Recollection, epitypifycation and multi-gene molecular analyses are needed for all type species of these genera in order to clarify their familial status. By illustrating and redescribing the type species we expect to stimulate interest for these fungi to be recollected. © 2014 Magnolia Press.
Yang L.,Guizhou Academy of Agricultural science |
Wang W.,Guizhou Academy of Agricultural science |
Yang W.,Guizhou Academy of Agricultural science |
Wang M.,Guizhou Academy of Agricultural science
Molecular Breeding | Year: 2013
The waxy (wx) gene in maize is associated with higher content of amylopectin in the endosperm and better flavor. The opaque-16 (o16) gene is associated with higher lysine content in the endosperm and better nutritional value. To pyramid the wx and o16 genes, cross and backcross populations were constructed using the o16 line QCL3024 and the two waxy lines, QCL5019 and QCL5008, as parents. The linkage marker umc1141 for the o16 gene and the internal marker phi027 for the wx gene were used to select the target genes. Simple sequence repeat markers covering the whole genome were used for background selection in individual progenies of the backcross population. The grain lysine content was determined using the Acid Orange-12 Dye Binding Lysine method. Qualitative and quantitative analyses of the grain content of amylopectin were performed using the I2-KI procedure and double-wavelength spectrophotometry, respectively. Four lines of the double recessive genotype wxwxo16o16 were obtained from the F4 generation of the cross population and three lines of the same genotype were obtained from the BC2F4 generation of the backcross population. The lysine content of the pyramid lines was 16-27 and 18-28 % higher than the waxy parents QCL5019 and QCL5008, respectively. The pyramid lines had 61-63 % more amylopectin than the high-lysine parent QCL3024. The three pyramid lines from the backcross population had similar genetic background to the waxy parent QCL5008. Our results are of significance for the improvement of maize quality. © 2013 Springer Science+Business Media Dordrecht.
Zhai R.,China National Rice Research Institute |
Feng Y.,China National Rice Research Institute |
Wang H.,ShenYang Agricultural University |
Zhan X.,China National Rice Research Institute |
And 8 more authors.
BMC Genomics | Year: 2013
Background: Heterosis is a phenomenon in which hybrids exhibit superior performance relative to parental phenotypes. In addition to the heterosis of above-ground agronomic traits on which most existing studies have focused, root heterosis is also an indispensable component of heterosis in the entire plant and of major importance to plant breeding. Consequently, systematic investigations of root heterosis, particularly in reproductive-stage rice, are needed. The recent advent of RNA sequencing technology (RNA-Seq) provides an opportunity to conduct in-depth transcript profiling for heterosis studies.Results: Using the Illumina HiSeq 2000 platform, the root transcriptomes of the super-hybrid rice variety Xieyou 9308 and its parents were analyzed at tillering and heading stages. Approximately 391 million high-quality paired-end reads (100-bp in size) were generated and aligned against the Nipponbare reference genome. We found that 38,872 of 42,081 (92.4%) annotated transcripts were represented by at least one sequence read. A total of 829 and 4186 transcripts that were differentially expressed between the hybrid and its parents (DGHP) were identified at tillering and heading stages, respectively. Out of the DGHP, 66.59% were down-regulated at the tillering stage and 64.41% were up-regulated at the heading stage. At the heading stage, the DGHP were significantly enriched in pathways related to processes such as carbohydrate metabolism and plant hormone signal transduction, with most of the key genes that are involved in the two pathways being up-regulated in the hybrid. Several significant DGHP that could be mapped to quantitative trait loci (QTLs) for yield and root traits are also involved in carbohydrate metabolism and plant hormone signal transduction pathways.Conclusions: An extensive transcriptome dataset was obtained by RNA-Seq, giving a comprehensive overview of the root transcriptomes at tillering and heading stages in a heterotic rice cross and providing a useful resource for the rice research community. Using comparative transcriptome analysis, we detected DGHP and identified a group of potential candidate transcripts. The changes in the expression of the candidate transcripts may lay a foundation for future studies on molecular mechanisms underlying root heterosis. © 2013 Zhai et al.; licensee BioMed Central Ltd.
Song M.,Nanjing Agricultural University |
Xu W.,Nanjing Agricultural University |
Xiang Y.,Nanjing Agricultural University |
Xiang Y.,Guizhou Academy of Agricultural science |
And 3 more authors.
Plant Molecular Biology | Year: 2014
Jacalin-related lectins (JRLs) are carbohydrate-binding proteins widely present in plants and have one or more jacalin domains in common. However, JRLs' structural types and functions are still poorly understood. In the present study, a total of 67 wheat (Triticum aestivum) JRL genes were identified through an exhausted search of EST database coupling with genome walking using published 454 sequence reads of Chinese Spring. A comparison of the translated wheat JRL proteins with those from other plants showed plant JRLs generally had low sequence similarity within and between species but exhibited conserved modular domain structures. More JRL genes encoded multiple jacalin domains in Arabidopsis thaliana, whereas more genes encoded chimeric JRLs in cereal plants. Dirigent domain-containing JRL genes were Poaceae-specific and accounted for nearly half of the identified wheat JRL genes. The dirigent domains were evolutionarily significantly correlated with the covalently linked jacalin domains. A phylogenetic analysis showed JRL proteins have experienced a substantial diversification after speciation. Moreover, new structural features conserved across the taxa were identified. Digital expression analysis and RT-PCR assays showed the expression of wheat JRL genes was largely tissue specific, typically low, and mostly inducible by biotic and abiotic stresses and stress hormones. These results suggest plant JRLs are critical for plant adaptation to stressful environments. © 2013 Springer Science+Business Media Dordrecht.
Wang J.,Chinese Academy of science |
Wang J.,University of Chinese Academy of Sciences |
Feng X.,Chinese Academy of science |
Anderson C.W.N.,Massey University |
And 3 more authors.
Plant and Soil | Year: 2014
Aims: The thiosulphate induced accumulation of mercury by the three plants Brassica juncea var.LDZY, Brassica juncea var.ASKYC and Brassica napus var. ZYYC and the transformation of mercury fractionation in the rhizosphere of each plant was investigated in the field. Methods: Experimental farmland was divided into control and thiosulphate plots. Each plot was divided into three subplots with each planted with one of the plants. After harvesting, the mercury concentration in plants, mercury fractionation in rhizosphere soil before and after phytoextraction, and the vertical distribution of bioavailable mercury in bulk soil profiles was analyzed. Results: The cultivar B. juncea var.LDZY accumulated a higher amount of mercury in shoots than the other two plants. Thiosulphate treatment promoted an increase in the concentration of metal in plants and a transformation of Fe/Mn oxide-bound and organic-bound mercury (potential bioavailable fractions) into soluble and exchangeable and specifically-sorbed fractions in the rhizosphere. The observed increase in bioavailable rhizosphere mercury concentration was restricted to the root zone; mercury did not move down the soil profile as a function of thiosulphate application to soil. Conclusions: Thiosulphate-induced phytoextraction has the potential to manage environmental risk of mercury in soil by decreasing the concentration of mercury associated with potential bioavailable fraction that can be accumulated by crop plants. © 2013 Springer Science+Business Media Dordrecht.