The Larix kaempferi genome reveals new insights into wood properties.

Here, through single-molecule real-time sequencing, we present a high-quality genome sequence of the Japanese larch (Larix kaempferi), a conifer species with great value for wood production and ecological afforestation. The assembled genome is 10.97 Gb in size, harboring 45,828 protein-coding genes. Of the genome, 66.8% consists of repeat sequences, of which long terminal repeat retrotransposons are dominant and make up 69.86%. We find that tandem duplications have been responsible for the expansion of genes involved in transcriptional regulation and stress responses, unveiling their crucial roles in adaptive evolution. Population transcriptome analysis reveals that lignin content in L. kaempferi is mainly determined by the process of monolignol polymerization. The expression values of six genes (LkCOMT7, LkCOMT8, LkLAC23, LkLAC102, LkPRX148, and LkPRX166) have significantly positive correlations with lignin content. These results indicated that the increased expression of these six genes might be responsible for the high lignin content of the larches' wood. Overall, this study provides new genome resources for investigating the evolution and biological function of conifer trees, and also offers new insights into wood properties of larches.

[Mechanism on differential gene expression and heterosis formation].

Despite the rediscovery of heterosis about a century ago and the suggestion of various genetic models to explain this phenomenon, little consensus has yet been reached about the genetic basis of heterosis. Following the genome organization variation and gene effects, an understanding of gene differential expression in hybrids and its parents provides a new opportunity to speculate on mechanisms that might lead to heterosis. Investigation on allele-specific gene expression in hybrid and gene differential expression between hybrids and its parents might contribute to improve our understanding of the molecular basis of heterosis and eventually guide breeding practices. In this review, we discussed the recent researches on allelic-specific expression in hybrid which was frequently observed in recent studies and analyzed its regulatory mechanism. All possible modes of gene action, including additivity, high- and low-parent dominance, underdominance, and over-dominance, were observed when investigating gene differential expression between hybrids and its parents. Data from transcriptomic studies screened several heterosis-associated genes and highlighted the importance of certain key biochemical pathways that may prove to be quintessential for the manifestation of heterosis. So far, no uniform global expression pat-terns were observed in these gene expression studies. Most heterosis-associated gene expression analyses have not revealed a predominant functional category to which differentially expressed genes belong. However, these gene expression profiling studies represent a first step towards the definition of the complex gene expression networks that might be relevant in the context of heterosis. New technique on gene expression profile and advancements in bioinformatics will facilitate our understanding of the genetic basis of heterosis at the gene-expression level.

Sequencing the genome of Marssonina brunnea reveals fungus-poplar co-evolution.

BACKGROUND: The fungus Marssonina brunnea is a causal pathogen of Marssonina leaf spot that devastates poplar plantations by defoliating susceptible trees before normal fall leaf drop. RESULTS: We sequence the genome of M. brunnea with a size of 52 Mb assembled into 89 scaffolds, representing the first sequenced Dermateaceae genome. By inoculating this fungus onto a poplar hybrid clone, we investigate how M. brunnea interacts and co-evolves with its host to colonize poplar leaves. While a handful of virulence genes in M. brunnea, mostly from the LysM family, are detected to up-regulate during infection, the poplar down-regulates its resistance genes, such as nucleotide binding site domains and leucine rich repeats, in response to infection. From 10,027 predicted proteins of M. brunnea in a comparison with those from poplar, we identify four poplar transferases that stimulate the host to resist M. brunnea. These transferas-encoding genes may have driven the co-evolution of M. brunnea and Populus during the process of infection and anti-infection. CONCLUSIONS: Our results from the draft sequence of the M. brunnea genome provide evidence for genome-genome interactions that play an important role in poplar-pathogen co-evolution. This knowledge could help to design effective strategies for controlling Marssonina leaf spot in poplar.

Effects of exogenous GABA on gene expression of Caragana intermedia roots under NaCl stress: regulatory roles for H2O2 and ethylene production.

gamma-aminobutyric acid (GABA) is a four-carbon non-protein amino acid presented in a wide range of organisms. In this study, a suppression subtractive hybridization (SSH) library was constructed using roots of a legume shrub, Caragana intermedia, with the combined treatment of 300 mm NaCl and 300 mm NaCl + 10 mm GABA. We obtained 224 GABA-regulated unique expressed sequence tags (ESTs) including signal transduction, transcriptional regulation, hormone biosynthesis, reactive oxygen species (ROS) and polyamine metabolism, etc. The key H(2)O(2)-generated genes, NADPH oxidase (CaGR60), peroxidase (CaGR61) and amine oxidase (CaGR62), were regulated at the mRNA level by 10 mm GABA, which clearly inhibited H(2)O(2) accumulation brought about by NaCl stress in roots and leaves with the observation of 3,3'-diaminobenzidine (DAB) staining. Similarly, 10 mm GABA also regulated the expression of 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase (ACO) genes (CaGR30 and CaGR31) and ethylene production in NaCl-treated roots. Surprisingly, these H(2)O(2)-generated genes were enhanced at the mRNA level by a lower concentration of GABA, at 0.25 mm, but not other alternative nitrogen sources, and endogenous GABA accumulated largely just by the application of GABA at either concentration. Our results further proved that GABA, as a signal molecule, participates in regulating the expression of genes in plants under salt stress.

[Biomass, carbon storage and nutrient characteristics in Larix kaempferi plantations at diffe-rent stand ages]. / ä¸åŒå¹´é¾„æ—¥æœ¬è½å¶æ¾äººå·¥æž—ç”Ÿç‰©é‡ã€ç¢³å‚¨é‡åŠå »åˆ†ç‰¹å¾.

Based on 7-, 17-, 30-, and 40-year-old Larix kaempferi plantations, this paper studied the influence of tree age on biomass, carbon storage and nutrient characteristics. There was significant difference in biomass and nutrient concentration of stem, bark, needle, branch and root at different development stages at individual tree level. The biomass of each organ showed a trend of increase with the increasing age. The concentrations of N, P, K decreased, Mg concentration increased at first and then decreased, and Ca concentration continued to rise with the increasing age. There was significant difference in biomass of each organ for dominant, intermediate and suppressed trees, but no significant difference in nutrient concentration. It indicated that nutrient concentration of each organ was not affected by competition. At stand level, the total biomass, carbon storage and nutrient accumulation increased with the increasing age. Compared with young stand, the growth rate of biomass, carbon storage and nutrient accumulation were increased by 217%, 218% and 56% in mature stand, respectively. It indicated L. kaempferi had a high nutrient use efficiency, and could utilize less nutrient to produce more dry matter. Except that the accumulation of P and K had a slight decrease in pre-mature stand (30 years old), other elements increased with the increasing age. N mainly concentrated in needle, Ca concentrated in stem, K and Mg concentrated in root and P was distributed evenly in different organs. The annual accumulation rates of biomass, carbon and nutrient of L. kaempferi stands decreased with the increasing age, from 7.16 t·hm-2, 3.40 t·hm-2 and 104.64 kg·hm-2 for young stand to 3.99 t·hm-2, 1.89 t·hm-2and 28.64 kg·hm-2 for mature stand, respectively. It indicated that L. kaempferi plantations had great carbon sequestration potential and high nutrient consumption during young and middle ages.

[Soil microorganisms, nutrients and enzyme activity of Larix kaempferi plantation under different ages in mountainous region of eastern Liaoning Province, China].

We studied the community of soil microorganisms, enzyme activity and soil nutrients under 11-, 20-, 34-and 47-year-old Larix kaempferi plantations in mountainous region of eastern Liaoning Province to discuss the soil biological properties of L. kaempferi plantations of different stand ages and their relationships with soil nutrients. The results showed that the indexes reflecting soil micro-organisms, enzyme activity and soil nutrients of L. kaempferi plantations were the highest under the 11- or 47-year-old stand and the lowest in the 20- or 34-year-old stand. Soil productivity appeared in a decline trend with the increasing stand age, and the changes of soil microbial community structure and enzyme activity were responsive to soil degradation. The difference of fungi community was more noticeable than that of bacteria community among the plantations with different stand ages. The results of CCA showed soil nutrient and pH had no effect on seasonal difference of community structure, but had effects on community, structure among different stand ages. The total N, organic carbon, C/N, available nitrogen, exchangeable Mg2+ and pH had greater effects on bacteria community, while available P, total K and pH had greater effect on fungi community among different age forests. The main T-RFs of bacteria and fungi had higher correlation with N and P, and the fungi community had higher correlation with organic carbon and K than bacteria community. The microor-ganism community of the 11- and 47-year-old stands had greater correlation with soil nutrients and enzyme activity than that of 20- and 34-year-old stands. Consequently, soil organisms, in particular soil fungi, could be used to indicate soil degradation.

Isolation, characterization and expression analysis of the BABY BOOM (BBM) gene from Larix kaempferi × L. olgensis during adventitious rooting.

The full-length cDNA and genomic sequences of the BABY BOOM (BBM) gene, designated LkBBM, were isolated from Larix kaempferi × Larix olgensis. The 3324 bp cDNA was cloned and its open reading frame (ORF) consists of 2370 nucleotides. The deduced 789 amino acid protein contains two AP2 domains and a BBM specific motif. Four conserved motifs between BBM and PLT were identified, which may be conducive to the similar function of BBM and PLT. The three dimensional (3D) structure of LkBBM was predicted and ß-sheets in the AP2-R2 domain of LkBBM might recognize the specific base pairs in the major groove. Analysis of the LkBBM gene structure indicates that the gene has eight introns and nine exons. In the 5'-flanking promoter region of LkBBM, many important potential cis-acting elements were identified, such as the TATABOX5 element (a functional TATA element), ROOTMOTIFTAPOX1 element (element of root specificity), AUXREPSIAA4 element (element involved in auxin responsiveness and gene expression in root meristem), MYB1AT element (element involved in MYB recognition), ARR1AT element (element involved in cytokinin responsiveness), GARE1OSREP1 element (element involved in gibberellin responsiveness) and PYRIMIDINEBOXHVEPB1 element (element involved in abscisic acid responsiveness), which all suggested that the expression of LkBBM is highly regulated. Compared with gene expression levels in the stem, stem tip and leaf, LkBBM shows a specific expression in the root, which indicates that LkBBM plays a key role in regulating the development and growth of root in larch. In the processing of larch adventitious root formation, LkBBM started to express on the eighth day after rooting treatment and its transcript level increased continuously afterwards. According to the gene characteristics, LkBBM is proposed as a molecular marker for root primordia of larch, and the initial period of LkBBM expression may be the formation period of root primordia in the processing of adventitious rooting of larch.

[Instant response of individual size inequality indices to thinning regimes in plantation].

Four kinds of thinning treatments were designed including thinning from below, thinning from above, mechanical thinning and crop tree release with the same thinning intensity on the 14-year-old pure Cunninghamia laceolata and Pinus massoniana plantations in Guangxi, and 6 kinds of size inequality indices were applied including stand deviation, variation coefficient, skewness, Gini coefficient, Kuznetz coefficient and Lorenz asymmetry coefficient to evaluate the change of individual volume inequality after the 4 kinds of thinning regimes applied. The results showed that stand deviation, variation coefficient, Gini coefficient and Kuznetz coefficient decreased and skewness increased after thinning from below or above compared with before thinning, while after crop tree release these four indices increased and skewness was uncertain. Lorenz asymmetry coefficient increased after thinning from below while it decreased after thinning from above or crop tree release compared with before thinning. There was no distinct rule for the 6 kinds of size inequality indices after mechanical thinning. The size inequality increased after crop tree release while it decreased af- ter thinning from above or below. The study suggested that Lorenz curve, Gini coefficient and Lorenz asymmetry coefficient could be used to compare the size inequality statically and dynamically among different stands, and could be discriminated the difference of size inequality caused by the different thinning regimes. Lorenz asymmetry coefficient even could be applied to tell the size inequality was mainly from the larger or smaller individuals. Crop tree release method in close-to-nature management could lessen the competition pressures of crop trees and increase the size inequality of the stand effectively which would be helpful to maintain the dominant position of crop trees.

[Effects of land use type on diurnal dynamics of environment microclimate in Karst zone].

In June 2007, the diurnal dynamics of light intensity, air temperature, air relative humidity, soil temperature, and surface soil (0-5 cm) water content of five land use types in the typical Karst zone of Lingyun City in Guangxi Zhuang Autonomous Region were observed. The results showed that different land use types altered the composition, coverage, and height of aboveground vegetation, which in turn changed the environment microclimate to different degree. The microclimate quality was in the order of forestland > shrub land > grassland > farmland > rock land. On rock land, the light intensity, air temperature, air relative humidity, soil temperature, and soil water content were higher, and the diurnal variation of the five climatic factors was notable, with the microclimatic conditions changed towards drier and hotter. Compared with those on rock land, the light intensity on forestland, shrub land, grassland, and farmland decreased by 96.4%, 52.0%, 17.0% and 44.2%, air temperature decreased by 30.1%, 20.2%, 12.7% and 17.8%, air relative humidity increased by 129.2%, 57.2%, 18.0% and 41.2%, soil temperature decreased by 11.5%, 8%, 2.5% and 5.5%, and soil water content increased by 42.6%, 33.2%, 15.7% and 14.0%, respectively. The five climatic factors on forestland and shrub land had lesser fluctuation, with the microclimate tended to cool and wet. Light intensity, air temperature, and soil temperature correlated positively with each other, and had negative correlations with air relative humidity and soil water content. A positive correlation was observed between air temperature and soil water content.

Development of male gametophyte of Larix leptolepis Gord. with emphasis on diffuse stage of meiosis.

A basic developmental framework of the Larix leptolepis Gord male gametophyte is presented in detail by squashing technique. The duration of the meiosis stage was more than 6 months, and included a long diffuse stage during winter. This long duration of the diffuse appearance of the diplotene stage makes L. leptolepis a unique suitable experimental material for studying the structure and function of the diffuse stage of meiosis. In particular, the processes of desynapsing and unpairing, which so far have received little attention, can be examined in detail. In L. leptolepis, the chromosomes undergo a dramatic structural reorganization during the diffuse diplotene stage. Based on the clearly visible differences in chromosome morphology, the diffuse diplotene stage was divided into four periods with suggested nomenclature as follows: schizonema, pre-diffuse diplotene, diffuse diplotene and post-diffuse diplotene. Both simultaneous and successive microsporogenesis were observed within L. leptolepis, and there was no strict relationship between the microsporogenesis types and the tetrad configurations, which are strongly influenced by spindle orientation, especially during meiosis II. The mature pollen grain at pollination consists of five cells aligned in an axial row. The prothallial cells cannot be regarded as senescent cells because they remain capable of division.