Phylogenomics is a new synthesized discipline which combines genomics with phylogenetics. Phylogenomics based on chloroplast genomes has shown many great advantages in plant phylogenetic research in recent years, providing resolutions for phylogeny of some taxonomically difficult groups of plants. However, there are some problems coming along with chloroplast phylogenomics as well. In this review, the application prospects and potential problems of chloroplast phylogenomics in plant phylogenetic reconstruction were discussed based on recent phylogenomic case studies. The influence of nextgeneration sequencing on chloroplast phylogenomics was also discussed.

WD repeats domain containing genes can participate in signal transduction, transcriptional regulation, RNA splicing and apoptosis and so on. WD repeats domain containing genes play important roles in plantpathogen interactions. SSR component and distribution in coding and regulation region of 94 WD repeats domain containing genes were analyzed in Magnaporthe oryzae, and the SSR variation in 7 coding regions of WD repeats domain containing genes was checked and analyzed its effect on secondary structure of protein. The result showed that abundance of SSRs were in the coding region and regulation region of WD repeats domain containing genes, but both SSR component and distribution were different among extron, intron, 5′UTR and 3′UTR; trinucleotide and hexanucleotide SSR in coding region were more than other region, and the frequency of hydrophilic amino acids was relatively higher. In additional, 7 SSR loci of coding region including SSR were polymorphism, and SSR polymorphism of these loci can affect the secondary structure of protein. The data of this study indicated that the mutation of SSR might play an important role for pathogenic gene mutation.

Anthers in flowers produce via meiosis haploid microspores, which mature to become pollen. However, pollen development at the molecular level is still not very clear. For the purpose of gaining understanding of the molecular control of pollen development, an Arabidopsis partial malesterility mutant ms1516 was reported previously, and the mutant gene MS1516 was mapped to a region of 28kb on chromosome 3 by a mapbased cloning approach. Here, we report that further bioinformatics analysis revealed that there was a meiosis related gene AtATM in this region. Allelism tests indicated that MS1516 and AtATM belonged to the same locus. Cell biology analysis showed that ms1516 mutant produced multiple uneven microspores during anther development, and most of which aborted at late stages. DAPI staining indicated that chromosome segregation was abnormal in ms1516 mutant meiocytes. Further scanning electron microscopy examination revealed abnormal pollen morphology formation in ms1516 mutant. Collectively these results demonstrated that MS1516 played an important role in tetrad formation and microspore development.

The populational signals derived from bacteria can induce plant resistance to pathogen or regulate plant development. Here we used 2D proteomics method to investigate Arabidopsis thaliana seedlings responding to OHHL, one of bacterial popular signals. After 2D proteomics and assay, we obtained 47 differential protein spots, most of their expression show increase with the extension of treatment time; these proteins are also involved in plant antioxidant activity, material metabolism and signal transaction. Therefore, we believe our results will show more insight into understanding the interactions mechanism of plant and microbe, and further well regulate plant themselves growth and development.

Erigeron breviscapus a medicinal plant was planted under different potassium levels to investigate effects of potassium on the growth and the accumulation of secondary metabolites, address the relationship between them in medicinal plants in the plantation. Results showed: In 0-0.372g/plant potassium levels, the biomass of E.breviscapus and yields of 2 active constituents, total caffeates and scutellarin, were significantly positively correlated with the amount of K fertilizer. Contents of total caffeates and scutellarin  were significantly positively correlated with the amount of K fertilizer from 0 to 0.248g/plant, but  negatively correlated with the amount of K fertilizer from 0.248 to 0.372g/plant. Contents of total caffeates and scutellarin were negatively correlated with contents of N in E.breviscapus, as predicated by the carbon/nutrient balance hypothesis. The findings suggest that: In condition of low potassium availability in soil more potassium fertilizer is possible to increase flavonoids accumulation in plant, but in high potassium availability is to reduce. Flavonoids accumulation in plants is not only found to increase in stress environment, but also in normal environment. There is not a tradeoff between the growth and accumulation of secondary metabolites in plant.

作为黄河三角洲关键建群物种之一，柽柳(Tamarix chinensis)在维持当地湿地生态系统平衡中起着重要作用。为更好地了解黄河三角洲柽柳居群的遗传结构和分化水平，本文利用10个ISSR分子标记，对来自三个柽柳居群的90个个体的遗传多样性进行了对比分析，结果表明：黄河三角洲的柽柳在物种水平存在较高的遗传多样性，总的多态位点百分率（P）达85%，Nei′s基因多样度(H)和Shannon′s多样性指数(I)分别为0.276和0.419；遗传变异主要存在于居群之内，居群间遗传分化程度低 (Gst=0.077, Φst=0.072)。这种遗传结构和分化格局的形成除了和柽柳的生活型、交配体系以及种子传播模式紧密相关外，可能还与其生境，特别是土壤的含盐量具有一定的关系。

A new species with two varieties, Meconopsis balangensis varieties balangensis and atrata (Papaveraceae), is described and characterized. Differences separating it from similar species are discussed and photos showing the diagnostic features are provided.

The anatomical structure of vegetative organs of Scutellaria amoena was studied by anatomy and fluorescent microscopy approaches. Results show that the primary xylem is diarch. The Casparian strip and starch grain can be clearly observed in the primary structure.  The distribution of prothenchyma is beside the vascular bundle of the stems and leaves. The prothenchyma groups in the more mature stem tissue are arranged into a ring. And the study of histological lacalization of flavonoids which has used the method of histochemistry shows that the pericycle and phloem in perennial root, and the parenchyma cells of epidermal and cortical in the stem and leaf, are the places where flavonoids is mainly accumulated. And the histochemistry results demonstrat that the color of relevant tissues in roots is deeper than in stems and leaves. The difference of anatomical structure between S.amoena and S.baicalensis is also discussed. The result shows that the mixed groups of prothenchyma are arranged in a relatively small area, but not into a ring in S.baicalensis. The thickening of the cell wall is not strongly. Prothenchyma is not found in the leaf of S.baicalensis, and the difference of histochemistry between these two shows that the content of flavonoids in S.amoena is higher than that in S.baicalensis. Therefore it is necessary to strengthen the comprehensive development and utilization on the endemics species S.amoena.

Chromosome numbers and karyotypes of 13 populations of six Oxytropis species (Fabaceae) from the QinghaiTibetan Plateau, China, were presented. The chromosome numbers and karyotypes in O.ochrocephala, O.tatarica, O.kansuensis and O.humifusa (2n=16) were reported for the first time. Bchromosomes were found from O.stracheyana (2n=48). The basic chromosome number of x=8 is confirmed for the genus. The available chromosomal data indicate that polyploidy may have played an important role in the evolution of the genus, with the incidence of polyploidy in the genus reaching 58%. However, our results indicated that among the populations here examined only one was a hexaploid with 2n=48. Such a chromosomal pattern indicates that the karyotypic repatterning at the diploid level seems to be the predominant feature of chromosomal evolution in the Oxytropis species from the QinghaiTibetan Plateau, and that sympatric speciation via hybridization and polyploidization has played a minor role in the species diversification of the genus from this area.

Based on statistical analysis of the characteristics of the vegetation in the dry valley in middle reaches of the Nujiang River in Tibet, it is revealed that: (1) There are 85 vascular plant species belonging to 55 genera in 34 families, including 4 ferns belonging to 4 genera in 4 families; 1 species of Gymnosperm; 79 species of Angiosperm belonging to 50 genera in 29 families. 13 arealtypes of the seed plants genera can be recognized, but mainly Pantropic (21.6%). 45 (57.0% of the total) species endemic to China are found, of which 42 (53.2%) species are endemic to SW China and 3 (3.8%) species endemic in Tibet. (2) Four main lifeforms, the Nanophanerophyte, the Hemicryptophyte, the Chamaephyte and the Therophyte, can be recognized, of which the Nanophanerophyte is highest, occupying 41. 2% and the Hemicryptophyte accounting for 40% of the total. (3) Based on the Raunkiaer frequency analysis, Sophora davidii, Sellaginella pulvinata, Cymbopogon distans, Sinopteris albofusca occurring in over 10 transect plots are among the highest frequency degrees with frequent percentage as 68.2%, 50.0%, 50.0%, 45.5%, respectively. (4) Based on the climate features and severity of drought, the characteristics of the ecological status, the living forms of communities with very low degree of plant coverage, the vegetation belongs to riparian arid desert type.

As an important component in montane moist forest ecosystems, bryophyte plays key roles in sustaining biodiversity and facilitating many ecological processes. The species composition and association of bryophytes on four substrates of CWD (coarse woody debris), canopy, forest floor and rock were investigated in middle mountain moist evergreen broadleaved forest in Ailao Mt., Yunnan. The results showed this region boasted a rich bryophyteflora which yielded 141 species belonging to 38 families and 69 genera, with Meteoriaceae (14 spp.) and Dicranaceae (13 spp.) predominating. 27 species appeared in more than 3 types of substrates. Host trunk had the largest number of species (94 spp.) among all substrate types. It found that there was a trend of bryophyte diversity decreased with increase of species association among dominant species of bryophyte at the level of microhabitat, based on the analysis of species association on different substrates in the natural forest.

Aquatic species and population in Chenghai Lake had been dramatically changed in recent two decades. Coverage percentage of aquatic vegetation had varied from a range of 24%-75% to that of 0.2%-85%; and its maximum distribution depth had increased from 4.5m to 5.5m; but the corresponding coverage area had been shrunk from 527.8hm2 to 73.05hm2;  the resource storage had reduced from 4766 tons to 314.53 tons. Analysis indicates that destruction of suitable habitat in southern part of the lake, pollution, eutrophication and unreasonable stocking grass carp were the main reasons causing the remarkable decay of aquatic vegetation. Protective measures had been proposed based on wetland restoration in southern part, pollutant reduction, prohibition of stocking grass carp, and control over pollution and eutrophication.

The seed traits, germinability and desiccation tolerance at different developing periods of Aquilaria sinensis seeds were studied in the present paper, the seed storage characteristics and effects of light and temperature on seed germination were investigated too. The results indicated that A.sinensis seeds reached the physiological maturation and got the maximum dryweight at 78d after anthesis, and seed germination percentage reached a peak at this period. Desiccation tolerance of embryos increased gradually from 57 to 85 days after anthesis and reached the maximum at 85d after anthesis. The optimal germination temperature was 25℃ to 35℃ and seed germination was inhibited by light in a certain degree. The germination percentage of A.sinensis seeds was only about 30% after stored in 4℃ for 30d when seed moisture content is 27.45%. However, the germination percentage was 53.33% after stored in 4℃ for 120d when dehydrated to the moisture content of 7.38%. Consequently, low temperature and reasonable dehydration were more suitable for seed shorttime storage. A.sinensis seeds could suffer dehydration in a certain degree, but the seed will damaged when dehydrated to the moisture content of 7.50%. Thus, A.sinensis seeds exhibited intermediate seed storage behavior.