Search

Pits in ray parenchyma cells are important to understand the functional anatomy of the ray parenchyma network in the xylem but have been less studied. Herein, pits in two types of ray parenchyma cells, contact cells and isolation cells, across different developmental stages were qualitatively studied using 48-year-old Populus tomentosa trees. The timing of differentiation and death was determined by histochemical staining and polarized light microscopy. The dimension, shape and density of pits as well as cell wall thickness were measured using SEM and optical microscopy images of semi-thin radial sections and macerated ray parenchyma cells, and analyzed by multi-factor analyses of variance. Results showed that secondary wall thickening and lignification of contact cells begun near the cambium, contrarily those of isolation cells have started until the transition zone. But even in the sapwood, contact cell walls were still much thinner than isolation cell walls. Moreover, district anatomical adaptions of pits during the xylem differentiation were present between horizontal walls and tangential walls, between contact cells and isolation cells. Ray pits were simple to slightly bordered, whereas sieve-like pits were only shown on tangential walls of isolation cells. Pit density of horizontal walls was similar between contact cells and isolation cells, nevertheless greater pits were present on tangential walls, especially for isolation cells. In addition, pits of ray parenchyma cells in the heartwood were smaller and more bordered than those in the sapwood, particularly on the horizontal walls. Moreover, isolation cells had pits with the smaller dimensions, greater pits on the tangential walls, more bordered pits on horizontal walls, as well as longer and narrower cell morphology with much thicker cell walls than contact cells. To a certain extent, all these anatomical adaptations were developed to ensure distinct functions of the two types of ray parenchyma cells in the xylem and finally to support tree growth in demand.

DNA barcoding technology has emerged as one of the most promising tools available to identify timber at the species level, contributing to the monitoring of the timber trade and the conservation of forestry sources. This paper reviews the progress, challenges, and existing problems in the development of DNA barcoding for wood identification in the last ten years. There is a focus on the optimization of DNA extraction methods for processed or ancient wood, the strategy of screening high-resolution DNA barcodes suitable for wood identification, the development of a wood DNA reference database especially for priority taxa, and the comparison and comprehensive application of sequence analytical methods to achieve accurate identification. In addition to DNA barcoding, the feasibility of other genetic methods for wood identification is also discussed. Furthermore, future research orientation and strategy of wood DNA barcoding are presented. We argue that wood DNA barcoding integrated with other methodologies including wood anatomy can offer an effective approach and a new perspective to promote legal logging for timber trade custody and global biodiversity conservation.

The isolation of wood DNA is a crucial step in the process of genetic identification of wood tissues and the current wood DNA extraction method is a limiting factor. For some valuable wood samples sent for forensic identification, the size of allowable sample is limited. Additionally, the identification process is so lengthy that it often cannot meet the needs of law enforcement. This study describes an optimized protocol that minimizes the sample size and duration of DNA extraction without decreasing the yield of DNA. Experiments on sample mass per extraction, sample lysis time and DNA precipitation time were carried out by a series of gradient tests. The amounts of DNA extracted were evaluated by the copy numbers of target DNA barcodes (rbcL and matK) from droplet digital PCR (ddPCR). It is the first to apply ddPCR technology to quantify and evaluate accurately DNA extracted from wood. The results indicated that 300 mg is an optimal sample mass when keeping the volume of DNA lysis buffer constant, which reduces the sample usage by 40%. Five hours is the optimal sample lysis time. Extending the duration of DNA precipitation does not significantly increase the amplicon yield from wood specimens of Pterocarpus erinaceus. The protocol developed in this study shortens the period of DNA extraction from wood tissues by approximately 58%. The amplicon yields obtained using the optimized method in this study indicate good extraction efficiency, and the wood samples sent for certification were identified as Pterocarpus erinaceus using the barcode combination matK+ndhF-rpl32+ITS2. This method will be suitable for the broad applicability of DNA identification and conservation of global wood resources.

Background Syringa pinnatifolia Hemsl. is a shrub belonging to the Oleaceae family. The peeled woody stems and roots of S. pinnatifolia are used in Chinese traditional medicine. This plant has been used for centuries, and modern pharmacological research has revealed its medicinal value. However, the wild populations of S. pinnatifolia have been decreasing, and it has been listed as an endangered plant in China. To elucidate the molecular mechanism leading to the synthesis of the major components of S. pinnatifolia for its further development and sustainable use, this study compared peeled stems and twigs at the metabolic and molecular levels. Results Peeled stems with the purple substance visible (SSP) and peeled twigs without the purple substance (TSP) were compared at different levels. Microscopic observation showed resin-like fillers in SSP and wood fiber cell walls approximately 1.0 μm thicker than those in TSP (wood fiber cell thickness approximately 2.7 μm). In addition, 104 volatile organic compounds and 870 non-volatile metabolites were detected in the non-targeted and widely-targeted metabolome analyses, respectively. Among the 76 differentially accumulated metabolites (DAMs) detected, 62 were up-accumulated in SSP. Most of these DAMs were terpenes, of which 90% were identified as sesquiterpenes in the volatile organic compound analysis. In the analysis of the non-volatile metabolites, 21 differentially accumulated lignans were identified, of which 18, including five subtypes, were accumulated in SSP. RNA sequencing revealed 4,421 upregulated differentially expressed genes (DEGs) and 5,522 downregulated DEGs in SSP compared with TSP, as well as 33,452 genes that were not differentially expressed. Analysis of the DEGs suggested that sesquiterpenes and lignans were mostly biosynthesized via the mevalonate and phenylpropanoid pathways, respectively. Additionally, in SSP, the enriched Gene Ontology terms included response to biotic stimulus and defense response, while the enriched Kyoto Encyclopedia of Genes and Genomes pathways included plant–pathogen interaction and many other pathways related to plant immunity. Conclusions This study provides metabolome and transcriptome information for S. pinnatifolia, suggesting that biotic stimuli, including pathogens, are potential and valuable approaches to promoting the biosynthesis of the metabolites linked to the medicinal properties of this plant.

A method for extraction of wood DNA and a strategy for designing high-resolution barcodes for wood were developed. Ycf1b was the prioritized barcode to resolve the Pterocarpus wood species studied. DNA barcoding, an effective tool for wood species identification, mainly focuses on universal barcodes and often lacks high resolution to differentiate species, especially for closely related taxa within the same genus. Therefore, more highly informative DNA barcodes need to be identified. This study is the first to report a strategy for developing specific DNA barcodes of wood tissues. The complete chloroplast genomes of leaf samples of three Pterocarpus species, i.e., P. indicus, P. santalinus, and P. tinctorius, were sequenced, and thereafter, the most variable DNA regions were identified on the scale of the complete chloroplast genomes. Finally, wood DNA was extracted from 30 wood specimens of the three Pterocarpus species, and DNA recovery rates of the selected regions were tested for applicability to verification on the wood specimens studied. The seven regions with the most variation (rpl32-ccsA, rpl20-clpP, trnC-rpoB, ycf1b, accD-ycf4, ycf1a, and psbK-accD) were identified from the chloroplast genome by quantifying nucleotide diversity (Pi > 0.02), which was remarkably higher than that of the plant universal barcodes (rbcL, matK, and trnH-psbA) and the previously reported barcodes (ndhF-rpl32 and trnL-F) used for phylogenetic analysis in Pterocarpus. After comprehensive evaluation of species discrimination ability and applicability, the ycf1b region performed well in terms of the recovery success rate (76.7%) and species identification (100%) for wood specimens of the three Pterocarpus species, and was identified as the preferred high-resolution chloroplast barcode for selected Pterocarpus species. It will offer technical support for curbing illegal timber harvesting activities and for conserving endangered and valuable wood species.

Made available in DSpace on 2019-10-04T12:13:41Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-05-01 National Natural Science Foundation of China National High-level Talent for Special Support Program of China China Scholarship Council Main conclusion Machine-learning approaches (MLAs) for DNA barcoding outperform distance- and tree-based methods on identification accuracy and cost-effectiveness to arrive at species-level identification of wood. DNA barcoding is a promising tool to combat illegal logging and associated trade, and the development of reliable and efficient analytical methods is essential for its extensive application in the trade of wood and in the forensics of natural materials more broadly. In this study, 120 DNA sequences of four barcodes (ITS2, matK, ndhF-rp132, and rbcL) generated in our previous study and 85 downloaded from National Center for Biotechnology Information (NCBI) were collected to establish a reference data set for six commercial Pterocarpus woods. MLAs (BLOG, BP-neural network, SMO and J48) were compared with distance- (TaxonDNA) and tree-based (NJ tree) methods based on identification accuracy and cost-effectiveness across these six species, and also were applied to discriminate the CITES-listed species Pterocarpus santalinus from its anatomically similar species P. tinctorius for forensic identification. MLAs provided higher identification accuracy (30.8-100%) than distance- (15.1-97.4%) and tree-based methods (11.1-87.5%), with SMO performing the best among the machine learning classifiers. The two-locus combination ITS2 + matK when using SMO classifier exhibited the highest resolution (100%) with the fewest barcodes for discriminating the six Pterocarpus species. The CITES-listed species P. santalinus was discriminated successfully from P. tinctorius using MLAs with a single barcode, ndhF-rp132. This study shows that MLAs provided higher identification accuracy and cost-effectiveness for forensic application over other analytical methods in DNA barcoding of Pterocarpus wood. Chinese Acad Forestry, Chinese Res Inst Wood Ind, Dept Wood Anat & Utilizat, Beijing 100091, Peoples R China Chinese Acad Forestry, Wood Collect WOODPEDIA, Beijing 100091, Peoples R China US Forest Serv, Forest Prod Lab, Ctr Wood Anat Res, USDA, Madison, WI 53726 USA Univ Wisconsin, Dept Bot, Madison, WI 53706 USA Purdue Univ, Dept Forestry & Natl Resources, W Lafayette, IN 47907 USA Univ Estadual Paulista, Ciencias Biol Bot, Botucatu, SP, Brazil Univ Estadual Paulista, Ciencias Biol Bot, Botucatu, SP, Brazil National Natural Science Foundation of China: 31600451 National High-level Talent for Special Support Program of China: W02020331 China Scholarship Council: 2017-3109

Reliable wood identification and proof of the provenance of trees is the first step for combating illegal logging. DNA barcoding belongs to the promising tools in this regard, for which reliable methods and reference libraries are needed. Machine learning approaches (MLAs) are tailored to the necessities of DNA barcoding, which are based on mathematical multivaried analysis. In the present study, eightDalbergiatimber species were investigated in terms of their DNA sequences focusing on four barcodes (ITS2,matK,trnH-psbA andtrnL) by means of the MLAs BLOG and WEKA for wood species identification. The data material downloaded from NCBI (288 sequences) and taken from a previous study of the authors (153 DNA sequences) was taken as dataset for calibration. The MLAs’ effectivity was verified through identification of non-vouchered wood specimens. The results indicate that the SMO classifier as part of the WEKA approach performed the best (98%~100%) for discriminating the eightDalbergiatimber species. Moreover, the two-locus combination ITS2+trnH-psbA showed the highest success rate. Furthermore, the non-vouchered wood specimens were successfully identified by means of ITS2+trnH-psbA with the SMO classifier. The MLAs are successful in combi- nation with DNA barcode reference libraries for the identification of endangeredDalbergiatimber species.

Made available in DSpace on 2018-11-26T15:47:17Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-01-31 Fundamental Research Funds of CAF National Natural Science Foundation of China China Postdoctoral Science Foundation China Scholarship Council DNA barcoding has been proposed as a useful tool for forensic wood identification and development of a reliable DNA reference library is an essential first step. Xylaria (wood collections) are potentially enormous data repositories if DNA information could be extracted from wood specimens. In this study, 31 xylarium wood specimens and 8 leaf specimens of six important commercial species of Pterocarpus were selected to investigate the reliability of DNA barcodes for authentication at the species level and to determine the feasibility of building wood DNA barcode reference libraries from xylarium specimens. Four DNA barcodes (ITS2, matK, ndhF-rpl32 and rbcL) and their combination were tested to evaluate their discrimination ability for Pterocarpus species with both TaxonDNA and tree-based analytical methods. The results indicated that the combination barcode of matK + ndhF-rpl32 + ITS2 yielded the best discrimination for the Pterocarpus species studied. The mini-barcode ndhF-rpl32 (167-173 bps) performed well distinguishing P. santalinus from its wood anatomically inseparable species P. tinctorius. Results from this study verified not only the feasibility of building DNA barcode libraries using xylarium wood specimens, but the importance of using wood rather than leaves as the source tissue, when wood is the botanical material to be identified. Chinese Acad Forestry, Chinese Res Inst Wood Ind, Dept Wood Anat & Utilizat, Beijing 100091, Peoples R China Chinese Acad Forestry, Wood Collect WOODPEDIA, Beijing 100091, Peoples R China USDA Forest Serv, Ctr Wood Anat Res, Forest Prod Lab, Madison, WI 53726 USA Univ Wisconsin, Dept Bot, Madison, WI 53706 USA Purdue Univ, Dept Forestry & Nat Resources, W Lafayette, IN 47907 USA Univ Estadual Paulista, Ciencias Biol Bot, Botucatu, SP, Brazil Chinese Acad Trop Agr Sci, Rubber Res Inst, Haikou 571737, Hainan, Peoples R China Univ Estadual Paulista, Ciencias Biol Bot, Botucatu, SP, Brazil Fundamental Research Funds of CAF: CAFYBB2017MA013 Fundamental Research Funds of CAF: CAFYBB2017ZE003 National Natural Science Foundation of China: 31600451 China Postdoctoral Science Foundation: 2016M590152 China Scholarship Council: 2016-3035

The wood samples of Populus euphratica Oliv. (Salicaceae) are common archaeological plant remains in the hot and arid regions of western China. However, it is difficult to identify P. euphratica wood based on traditional wood anatomical methods alone. DNA barcoding might provide a higher security for species identification. In this study, aged wood specimens stored for approximately 30, 60, and 80 years and archaeological wood up to 3600 years old were in focus to explore the potential of DNA extraction and PCR amplification for different-sized fragments, ranging between 100 and 800 bp, taken from wood stored for different periods. The results indicated that DNA fragments of more than 100 bp could be successfully retrieved from a wood specimen stored for about 80 years based on a modified Qiagen kit protocol. However, it was impossible to obtain DNA segments from the 3600-year-old wood according to the current extraction protocol. Moreover, it was deduced that two-stage PCR amplification could play a significant role in the analysis of DNA retrieved from aged wood materials. With the aid of phylogenetic analysis, based on the short DNA barcode rbcL-2 of 202 bp in length, it was possible to differentiate P. euphratica from the other species of the Populus genus.

Made available in DSpace on 2018-11-26T15:45:37Z (GMT). No. of bitstreams: 0 Previous issue date: 2017-12-01 China Postdoctoral Science Foundation National Natural Science Foundation of China Fundamental Research Funds of Chinese Academy of Forestry China Scholarship Council U.S. State Department Interagency Agreement ITS2+ trnH - psbA was the best combination of DNA barcode to resolve the Dalbergia wood species studied. We demonstrate the feasibility of building a DNA barcode reference database using xylarium wood specimens. The increase in illegal logging and timber trade of CITES-listed tropical species necessitates the development of unambiguous identification methods at the species level. For these methods to be fully functional and deployable for law enforcement, they must work using wood or wood products. DNA barcoding of wood has been promoted as a promising tool for species identification; however, the main barrier to extensive application of DNA barcoding to wood is the lack of a comprehensive and reliable DNA reference library of barcodes from wood. In this study, xylarium wood specimens of nine Dalbergia species were selected from the Wood Collection of the Chinese Academy of Forestry and DNA was then extracted from them for further PCR amplification of eight potential DNA barcode sequences (ITS2, matK, trnL, trnH-psbA, trnV-trnM1, trnV-trnM2, trnC-petN, and trnS-trnG). The barcodes were tested singly and in combination for species-level discrimination ability by tree-based [neighbor-joining (NJ)] and distance-based (TaxonDNA) methods. We found that the discrimination ability of DNA barcodes in combination was higher than any single DNA marker among the Dalbergia species studied, with the best two-marker combination of ITS2+trnH-psbA analyzed with NJ trees performing the best (100% accuracy). These barcodes are relatively short regions (< 350 bp) and amplification reactions were performed with high success (ae90%) using wood as the source material, a necessary factor to apply DNA barcoding to timber trade. The present results demonstrate the feasibility of using vouchered xylarium specimens to build DNA barcoding reference databases. Chinese Acad Forestry, Chinese Res Inst Wood Ind, Dept Wood Anat & Utilizat, Beijing 100091, Peoples R China Chinese Acad Forestry, Wood Collect WOODPEDIA, Beijing 100091, Peoples R China US Forest Serv, Ctr Wood Anat Res, USDA, Forest Prod Lab, Madison, WI 53726 USA Univ Wisconsin, Dept Bot, Madison, WI 53706 USA Purdue Univ, Dept Forestry & Nat Resources, W Lafayette, IN 47907 USA Univ Estadual Paulista, Ciencias Biol Bot, Sao Paulo, Brazil Univ Estadual Paulista, Ciencias Biol Bot, Sao Paulo, Brazil China Postdoctoral Science Foundation: 2016M590152 National Natural Science Foundation of China: 31600451 Fundamental Research Funds of Chinese Academy of Forestry: CAFYBB2017ZE003 China Scholarship Council: 2016-3035 U.S. State Department Interagency Agreement: 19318814Y0010-140001-0001/P00001

Aquilaria sinensis (Lour.) Gilg is an evergreen tree and produces agarwood used for incense and as a uniquely precious medicine. It is in danger of disappearing due to illegal logging and its identification and protection is crucial. However, it is difficult or impossible to distinguish A. sinensis from other species of the genus Aquilaria Lam. and its closely related genus Gyrinops Gaertn. based on wood anatomical characteristics. Probably, DNA barcoding technology might provide an improvement in species identification. In this study, wood samples were tested, which were submitted to high-temperature drying and were stored for a long period in a xylarium. The factors should be identified that hinder the efficiency of wood DNA extraction from this species. The results indicate that the DNA from the wood tissues could be successfully amplified, apart from some DNA regions from the heartwood of the dried samples and the xylarium samples. The DNA sequences from the wood tissues mostly matched with the sequences of A. sinensis deposited in the GenBank. Moreover, analyses of phylogenetic trees based on trnL-trnF and ITS1 regions indicated that the wood tissues in the tests clustered together with the A. sinensis species from the GenBank, with bootstrap values of 74% and 94%, respectively. Consequently, it is feasible to identify A. sinensis wood on a species level based on the DNA barcoding technology.

Agarwood, a compound substance of xylem tissue and its inclusions, is generally formed in some genera of Thymelaeaceae (e.g., Aquilaria) during the tree’s natural growing process. Due to the medicinal and economic values of agarwood augmented by unsustainable harvesting techniques, calls have been made by international bodies such as CITES and IUCN to conserve agarwood-producing tree species. Consequently, identification of agarwood resources becomes an important issue to provide better protection for the species. In this chapter, we review the status, i.e., forest resources, wood features, identification, and market development of agarwood (Aquilaria) in China. Some suggestions for the sustainable development of Aquilaria resources in China are also provided.

Based on the reality of construction business and the basic theory of commercial bank credit ratings, according to the characteristics and actual situation of China's construction enterprises, this paper analyzed the existing rating methodology and theoretical basis, mergingthe fuzzy comprehensive model into enterprises credit ratings, expecting to construct a credit rating index system model for the realities of construction enterprises, providing credible and reliable data for the credit management, forecasting of current credit situation and risk aversion, providing modeling tools for the credit rating and credit risk control of China's construction enterprises, especially small and medium companies and propose corresponding rating management measures.

DNA was isolated from the sapwood, transition wood and heartwood of fresh and dried Cunninghamia lanceolata wood using two DNA extraction protocols: the modified CTAB method and the modified Qiagen kit. Our major objective was to (i) determine an optimized method for retrieving good quality and sufficient quantity of DNA from wood, and to (ii) investigate the effect of different radial positions of fresh and dried wood for DNA extraction. In comparison with the modified CTAB method, a greater quantity of higher quality DNA – both chloroplast and nuclear ribosomal DNA – was retrieved using the Qiagen kit protocol. The chloroplast DNA regions retrieved from both fresh and dried wood were successfully amplified using both protocols, but the PCR amplification for the rDNA-ITS region from the heartwood failed using both protocols. The quantity and purity of the DNA from the sapwood and transition wood (derived from nuclei and plastids in the parenchyma cells) was greater than that from the heartwood (derived mainly from amyloplasts). Due to the influence of the drying treatment, the quantity of DNA decreased by more than 50%. The optimized radial position for DNA extraction in the stem was demonstrated based on anatomical observation.