Short Communication: Using ITS as a molecular marker for Mangifera species identification in Central Sumatra

Abstract

The relationship among Mangifera species in Central Sumatra is currently unclear. Previous molecular studies on these taxa using cpDNA were unable to produce well-resolved phylogenetic trees. In this study, we explored the potential of the ITS sequences as molecular markers for Mangifera species to better resolve the phylogenetic analysis. Parsimony analysis revealed that the common ancestor M. quadrifida as the first species appeared in Central Sumatra. Mangifera sp. which assumed as new species had the longest genetic distance among species examined and may assumed as the most primitive species of Mangifera in Neighbor-Joining analysis. M. sumatrana and M. torquenda were closely related as well as M. foetida and M. odorata. Also, M. indica was closely related to M. kemanga. This finding and the other marker of cpDNA such as trnL-F and rbcL gene may suggest a possibility to revision in the latest Mangifera classification based on morphological character. Our results also revealed and support the genus Mangifera is a monophyletic group.

Phylogenetic analysis of Mangifera from central region of Sumatra using trnL-F intergenic spacer

“…However, Fitmawati and Hartana (2010), also used trnL-F intergenic spacer for Mangifera from Sulawesi, did not agree with that statement and stated that M. laurina was different species from M. Indica, also, M. laurina was the ancestor for M. indica which is the cultivated form of M. laurina. This result also contrasts with the previous study using ITS sequence (Fitmawati et al 2016) which stated that M. odorata has a close relationship with M. foetida.…”

Determination of phylogenetic relationships in the genusMangiferabased on whole chloroplast genome and nuclear genome sequences

“…Determination of phylogenetic relationships among crop species provides basic information for predicting their evolutionary history, taxonomical classification, evaluating their diversity and importance in plant breeding (Zhang et al 2012). Although genetic analysis of plants has improved rapidly with advanced sequencing technology, many phylogenetic studies in the genus Mangifera have relied on a set of molecular markers such as amplified fragment length polymorphisms (AFLP), rapid amplified polymorphic DNA (RAPD) and simple sequence repeats (SSR) and the sequencing of limited numbers of targeted regions in the chloroplast genome (maturase K, trnL-F spacer regions) and nuclear ribosomal DNA (internal transcribed spacer/ITS region) (Eiadthong et al 1999;Fitmawati et al 2017;Fitmawati 2016;Hartana 2010;Hidayat et al 2011;Schnell and Knight Jr 1992;Yonemori et al 2002). This is the first comparative analysis of phylogenetic relationship within the genus using both whole chloroplast genomes and multiple single-copy nuclear genes.…”

“…Recent studies have used molecular markers targeting coding and non-coding regions in the chloroplast genome (Eiadthong et al 1999;Fitmawati et al 2017;Hartana 2010;Hidayat et al 2011) and a set of nuclear genes (Fitmawati 2016;Schnell and Knight Jr 1992;Yonemori et al 2002) to analyse phylogenetic relationships within the genus. However, the results have not been consistent, and many studies were unsuccessful in inferring evolutionary relationships with fully resolved phylogenies.…”

Short Communication: Update phylogenetic information of the local varieties of cloves (Syzygium aromaticum) from North Maluku, Indonesia based on ITS sequences data

“…It is also easy to be amplified using universal primers, has high sensitivity due to its small size (300-800 bp) and high copy number in the genome (100-200 copies) (Baldwin et al 1995). It has been proven to be a useful source of informative characters for genetic variability and phylogenetic studies in many Angiosperm families (Baldwin et al 1995;Yonemori et al 2002;Biffin et al 2007;Fitmawati 2016;Wilson and Heslewood 2016;Hapsari et al 2018). Hence, it was expected that the use of ITS gene sequences will produce the best phylogenetic tree model which are useful for further conservation and breeding programs of native cloves in Indonesia.…”