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• W1025986433 abstract "Dipterocarpaceae is the main timber family of tropical forest trees in the Malesian region with a geographical distribution that extends to South America and Africa. The family comprises approximately 500 species in 17 genera and is subdivided into three subfamilies: Dipterocarpoideae, Monotoideae and Pakaraimoideae (Ashton, 1982). Dipterocarpoideae is the richest in species with a total of 470 species in 13 genera (Ashton, 1982). Dipterocarpoideae is divided into two tribes: Dipterocarpeae and Shoreae. The genera of Dipterocarpeae are Anisoptera, Cotylelobium, Dipterocarpus, Stemonoporus, Upuna, Vateria and Vateriopsis, while those of Shoreae are Dryobalanops, Hopea, Neobalanocarpus, Parashorea and Shorea. Shorea and Hopea contain most species; 169 in the former and 100 in the latter. Molecular phylogenies of the subfamily Dipterocarpoideae have been studied since 1998, especially the genus Shorea and its sister genera in tribe Shoreae, because this genus has the highest number of species and the most valuable timber of the Dipterocarpaceae. Many of these species are endangered. The purpose of molecular phylogenies is to complement phylogenies based on morphology as there is still a debate on the placement of some genera in the tribe Dipterocarpoideae. The classification of Shorea in this research refers to Ashton (1982) and Symington (1943). Symington (1943) has divided Shorea based on wood color (White Meranti, Yellow Meranti, Balau and Red Meranti). Asthon (1982) has generally retained the classification by Symington (1943), but some of the groups were reclassified into lower taxonomical ranks. The need for identification tools for Dipterocarpacae in order to avoid fraud in certifying the family’s timber has led to an improvement in modern identification systems that use molecular data. Traditionally, Dipterocarpaceae are recognized based on their morphological characters, but sometimes these characters have constraints, particularly in the absence of a flower, the most useful taxonomic identification character for the dipterocarps. The abundance of molecular data as well as advanced technologies in DNA sequencing have made DNA barcoding a widely-used practice in many different fields of taxonomic studies, not as a replacement but as a complement to traditional taxonomy and to accelerate the identification process. Another advantage of the large number of sequences available in public data bases as the NCBI database is that it can lead to a new concept of species identification through the development of a molecular taxonomic key. However, since DNA barcoding methods are still in their infancy, the database for DNA barcoding is still being established. This study aims to infer the phylogenetic relationships of the members of the subfamily Dipterocarpoideae and to study the placement of the genera based on four chloroplast regions (trnL intron, psbC-trnS IGS, matK and rbcL). Furthermore, the suitability of the two barcoding regions (matK and rbcL) will be evaluated, which were proposed by the Consortium for the Barcode of Life (CBOL) in 2009. This study also aims to develop a taxonomic identification key based on the phylogenetic analysis for species identification purposes. Dipterocarpacae sequences that were deposited in the NCBI database were retrieved for four chloroplast regions (trnL intron, psbC-trnS IGS, matK and rbcL). In addition to the analysis of the sequences from the NCBI database, we also sequenced samples of dipterocarps available at the section Forest Genetics and Forest Tree Breeding, Georg-August-University Göttingen, at the four chloroplast regions in order to analyze the highest possible number of species. The phylogenetic analysis was done using MEGA 5 software and the statistical methods of maximum parsimony (MP), maximum likelihood (ML) and neighbor joining (NJ). For the DNA-based identification analyses, we evaluated the suitability of the two barcode regions using nBLAST, and performed the phylogenetic analysis using the neighbor joining method. Our results succeeded in obtaining sequences for various numbers of species for each studied chloroplast region, namely 145 species for the trnL intron, 117 species for the psbC-trnS IGS, 116 species for the matK region and 67 species for the rbcL region. The final length of the sequences varied for each region, 537 bp, 1136 bp, 653 bp and 647 bp for the trnL intron, psbC-trnS IGS, matK and rbcL, respectively. For the phylogenetic analyses, MP, ML and NJ analyses of cpDNA sequences produced similar tree topologies. As a result, our discussion is mostly based on the results of the MP analysis. Generally, the evolutionary relationships within the subfamily Dipterocarpoideae could not be clearly revealed by the four chloroplast regions. The regions were able to resolve the tribes Dipterocarpeae and Shoreae, but were less successful within the tribes, particularly Shoreae. For the genus Dipterocarpus, recent studies only provide sequence data for the regions trnL intron and matK. We observed two distinct groups comprising species of this genus for both gene regions. There is an assumption that Dipterocarpus may represent the basal clade of Dipterocarpoideae (Meijer, 1979). The name of this family was taken based on this genus, possibly because it is regarded as a primitive group among Dipterocarpaceae’s members (Maury - Lechon, 1979). This genus is well defined in the Dipterocarpaceae family based on morphological characters and molecular analyses. The psbC-trnS IGS region in this study agreed with previous research by Symington (1943) in its ability to form a monophyletic group based on wood color in the genus Shorea. The matK region showed the best ability to delineate the relationships of the tribe Dipterocarpeae and succeeded in distinguishing section Doona of Shorea as a monophyletic group. However, this region failed to work as well in classifying other members of Shoreae. Despite the rbcL region’s status as the first DNA region to be sequenced from a chloroplast region, there are few rbcL sequences available for dipterocarps in the NCBI database. The results based on the data from the laboratory showed that this region was unable to trace the evolutionary relationship of Dipterocarpoideae below the generic level. The matK region in this study showed that the genus Dryobalanops has an affinity with genus Dipterocarpus, while the trnL intron tree showed that Dryobalanops is close to section Balau of the Shorea group. These contradictory results support the assumption of Indrioko (2005) that this genus is a basal clade of tribe Shoreae. The DNA-based identification was studied using two approaches, namely DNA barcoding and a molecular taxonomic identification key. The two DNA barcode regions, matK and rbcL, adopted from the Consortium for the Barcode of Life for land plants (Hollingsworth et al., 2009), were applied to assess the feasibility of these regions as barcodes to discriminate the Dipterocarpaceae. Most information for the matK region was available in the NCBI database, but additional samples were also included in this study. In total, 119 and 67 samples were studied using the matK and rbcL regions, respectively. The effectiveness of the barcode analysis in this study was assessed by the formation of monophyletic groups of the query sequences and the reference sequences which are deposited in NCBI using neighbor joining trees and then searching for the similarity of the query sequences from the laboratory against the available data in the NCBI database using nBLAST. Although the neighbor joining tree placed some of the sequences in the correct genus, this region could not clearly separate the genera Shorea, Hopea and Parashorea into one distinct group for each of them. The nBLAST analysis resulted in most of the query sequences leading to misidentification at the species level. Because of the low ability of the matK region for species discrimination, as indicated by nBLAST and phylogenetic analysis, along with the difficulty in amplifying it, makes this region unsuitable as a barcode region for Dipterocarpaceae. Regarding the rbcL region, we could not observe any affiliation of the query sequences from the laboratory since only several sequences of this region are available in the databases. However, based on our neighbor joining analysis, we observed that this region is able to discriminate above the generic level but not the specific level. DNA-based identification using a taxonomic identification key indicated that the approach is not yet a suitable tool to discriminate species. Many species belonging to the same haplotype were detected when constructing the key. A possible reason for this is the use of the trnL intron region to construct the key. Taberlet et al., (2007) has reported that this region is not effective in distinguishing closely-related species." @default.
• W1025986433 created "2016-06-24" @default.
• W1025986433 creator A5077175778 @default.
• W1025986433 date "2022-02-20" @default.
• W1025986433 modified "2023-10-18" @default.
• W1025986433 title "DNA sequence-based Identification and molecular phylogeni within subfamily Dipterocarpoideae (Dipterocarpaceae)" @default.
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