Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China.
Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China.
Planta. 2019 Jul;250(1):95-104. doi: 10.1007/s00425-019-03150-1. Epub 2019 Mar 28.
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.
开发了一种提取木材 DNA 的方法和设计木材高分辨率条形码的策略。Ycf1b 被优先选为解决所研究的紫檀木种的条形码。DNA 条形码是一种有效的木材物种鉴定工具，主要侧重于通用条形码，往往缺乏区分物种的高分辨率，特别是对于同一属内的密切相关分类群。因此，需要鉴定更多信息量高的 DNA 条形码。本研究首次报道了一种开发木材组织特定 DNA 条形码的策略。对三种紫檀属植物（紫檀、檀香和紫檀）叶片样本的完整叶绿体基因组进行了测序，然后在完整叶绿体基因组的尺度上确定了最具变异性的 DNA 区域。最后，从这三种紫檀木的 30 个木材标本中提取了木材 DNA，并测试了所选区域的 DNA 回收率，以验证对所研究木材标本的适用性。通过量化核苷酸多样性（Pi>0.02），从叶绿体基因组中鉴定出了七个具有最多变异的区域（rpl32-ccsA、rpl20-clpP、trnC-rpoB、ycf1b、accD-ycf4、ycf1a 和 psbK-accD），这显著高于植物通用条形码（rbcL、matK 和 trnH-psbA）和先前报道的用于紫檀属系统发育分析的条形码（ndhF-rpl32 和 trnL-F）。在综合评估物种区分能力和适用性后，ycf1b 区域在三种紫檀木木材标本的回收成功率（76.7%）和物种鉴定（100%）方面表现良好，被确定为所选紫檀属物种的首选高分辨率叶绿体条形码。它将为遏制非法木材采伐活动和保护濒危和有价值的木材物种提供技术支持。
