Pandan (Pandanus sp), Rotan (Calamus sp), and Rengas (Gluta sp) from Kajuik Lake, Riau Province, Indonesia

Abstract

Pandan (Pandanus sp), Rotan (Calamus sp), and Rengas (Gluta sp) are the three most important plants growing at Kajuik Lake, Langgam, Riau Province, Indonesia; however, their species names have not been identified. This study aimed to identify their species names using nuclear internal transcribed spacer (ITS) and psbA-trnH intergenic spacer sequences. The method employed was DNA isolation from fresh leaves, PCR using primer pairs of ITS region for Pandanus sp and psbA-trnH intergenic spacer for Calamus sp and Gluta sp, electrophoresis, sequencing, and data analysis using BLASTn program and MEGA software version 6.0. Pandanus tectorius was the only one accession that was similar to Pandanus sp with the identity was 90%, however the query cover was too small, only 39%. On the contrary, Calamus sp showed the highest genetic similarity to Calamus travancoricus, but in fact, both were differed morphologically. There was no database of psbA-trnH intergenic spacer sequence available for species in Gluta. In conclusion, the species names for those plants still could not be determined. It because they might be the identified plants but their sequences databases were not available in large quantities or they were new species which had never been identified and published in public database.

Confirmation of Tuntun Angin (Elaeocarpus floribundus) Taxonomic Status Using matK and ITS Sequences

“…If the identity value does not reach 100%, then the species' name or taxonomic status of sample observed can not be determined. In addition, this study also showed that the molecular identification technique should be supported by the availability and the abundance of DNA sequences database (Will & Rubinoff, 2004;DeSalle, 2006;Hajibabaei et al, 2007;Roslim, 2016), due to the fact that DNA sequence of organism identified must be aligned and compared to the DNA sequence database which was generated from known species (Hajibabaei et al, 2007). Until now (updated in October 1 st , 2016), the DNA sequences database of Elaeocarpus which are available in GenBank have been very abundant, i.e.…”

“…The PCR products of matK and ITS fragments ( Figure 3) were thick enough for sequencing requirement. The thick and single band of PCR products will produce good sequences (Nugraha et al, 2014;Roslim et al, 2016a;Roslim, 2016).…”

“…However, the ITS sequence of tuntun angin was not similar to ITS sequence of E. floribundus because there was no database of the sequence in GenBank. This study showed that the determination of a plant species' name using the molecular identification technique must consider some BLAST parameters, for example, high max score, high total score, high query cover, low E-value (0.0), and 100% identity (Madden, 2013;Roslim, 2016;Roslim et al, 2016a). If the identity value does not reach 100%, then the species' name or taxonomic status of sample observed can not be determined.…”

“…Kajuik Lake is part of the floodplain ecosystem of Kampar River located in Langgam, Pelalawan Regency, Riau Province, Indonesia. Various plants -suggested endemic to Riau -grow in Kajuik Lake, such as rattan (Calamus sp), renghas (Gluta sp), pandan (Pandanus sp), durik-durik (Syzygium sp), and tuntun angin (Elaeocarpus floribundus) (Elvyra & Yus, 2012;Roslim, 2016;Roslim et al, 2016a).…”

THE ABILITY OF matK AND trnL-trnL-trnF INTERGENIC SPACER TO DISCERN CERTAIN SPECIES ACCESSIONS OF THE FAMILIES SOLANACEAE AND FABACEAE

“…Unfortunately, DNA barcode sequences of several species members of families Solanaceae (such as S. ferox) and Fabaceae (like A. microcarpum and A. pauciflorum) are unavailable in the public database. This situation potentially complicates and aborts the identification using DNA barcoding since the DNA barcoding analysis needs the availability of abundant DNA sequences in the public database (Roslim, 2018). Therefore, this study aims to analyze the DNA barcodes matK and trnL-trnL-trnF IGS in several species of Solanaceae and Fabaceae.…”