Saddhe Ankush Ashok, Jamdade Rahul Arvind, Kumar Kundan
Department of Biological Sciences, Birla Institute of Technology and Science Pilani, K. K. Birla Goa Campus, Sancoale, Goa 403726 India.
Department of Zoology, Yashwantrao Chavan Institute of Science, Satara, Maharashtra 415001 India.
Springerplus. 2016 Sep 13;5(1):1554. doi: 10.1186/s40064-016-3191-4. eCollection 2016.
Mangroves are salt-tolerant forest ecosystems of tropical and subtropical intertidal regions. They are among most productive, diverse, biologically important ecosystem and inclined toward threatened system. Identification of mangrove species is of critical importance in conserving and utilizing biodiversity, which apparently hindered by a lack of taxonomic expertise. In recent years, DNA barcoding using plastid markers rbcL and matK has been suggested as an effective method to enrich traditional taxonomic expertise for rapid species identification and biodiversity inventories. In the present study, we performed assessment of available 14 mangrove species of Goa, west coast India based on core DNA barcode markers, rbcL and matK. PCR amplification success rate, intra- and inter-specific genetic distance variation and the correct identification percentage were taken into account to assess candidate barcode regions. PCR and sequence success rate were high in rbcL (97.7 %) and matK (95.5 %) region. The two candidate chloroplast barcoding regions (rbcL, matK) yielded barcode gaps. Our results clearly demonstrated that matK locus assigned highest correct identification rates (72.09 %) based on TaxonDNA Best Match criteria. The concatenated rbcL + matK loci were able to adequately discriminate all mangrove genera and species to some extent except those in Rhizophora, Sonneratia and Avicennia. Our study provides the first endorsement of the species resolution among mangroves using plastid genes with few exceptions. Our future work will be focused on evaluation of other barcode markers to delineate complete resolution of mangrove species and identification of putative hybrids.
红树林是热带和亚热带潮间带地区耐盐的森林生态系统。它们是生产力最高、生物多样性最丰富、生物学意义最重要的生态系统之一，且面临受到威胁的趋势。红树林物种的鉴定对于保护和利用生物多样性至关重要，但显然因缺乏分类学专业知识而受到阻碍。近年来，使用质体标记rbcL和matK的DNA条形码技术被认为是一种有效的方法，可以丰富传统分类学专业知识，用于快速物种鉴定和生物多样性清查。在本研究中，我们基于核心DNA条形码标记rbcL和matK对印度西海岸果阿邦的14种红树林物种进行了评估。考虑了PCR扩增成功率、种内和种间遗传距离变异以及正确鉴定百分比，以评估候选条形码区域。rbcL区域（97.7%）和matK区域（95.5%）的PCR和测序成功率较高。这两个候选叶绿体条形码区域（rbcL、matK）产生了条形码间隙。我们的结果清楚地表明，基于TaxonDNA最佳匹配标准，matK位点的正确鉴定率最高（72.09%）。除了红树属、海桑属和白骨壤属中的物种外，串联的rbcL + matK位点在一定程度上能够充分区分所有红树林属和物种。我们的研究首次证实了使用质体基因在红树林物种分辨率方面的有效性，仅有少数例外情况。我们未来的工作将集中在评估其他条形码标记，以描绘红树林物种的完整分辨率，并鉴定假定的杂交种。
