The genetic diversity within and among populations of Shorea leprosula and Shorea parvifolia from Indonesia was investigated using amplified fragment length polymorphisms (AFLPs). The results indicated that S. leprosula is genetically more variable than S. parvifolia. At the population level, a higher level of genetic diversity was revealed for S. leprosula with a percentage of polymorphic loci (PPL p ) of 53.32% and an expected heterozygosity (H ep ) of 0.16 in comparison with S. parvifolia showing PPL p of 51.79% and H ep of 0.14. At the species level, S. leprosula showed PPL s of 92.86% and H es of 0.21, while S. parvifolia showed PPL s of 85.71% and H es of 0.21. Genetic differentiation (G st ) indicated that 25 and 31% of total genetic diversity in S. leprosula and S. parvifolia, respectively, were attributed to the differences among populations. An analysis of molecular variance (AMOVA) at two hierarchical levels exhibited that most genetic variation resided within populations with proportion of 70.2% for S. leprosula and 66.2% for S. parvifolia. The AMOVA at three hierarchical levels performed for S. leprosula and S. parvifolia together revealed that the genetic difference between the two species was remarkably higher with a proportion of 44.1% than the differences within and among populations (38.1 and 17.8%, respectively). The genetic differentiation between islands was significant for S. leprosula but not for S. parvifolia. The observed genetic diversity agreed with the life history traits of Shorea species. Highly differentiating individual AFLP markers were found for each species, which will serve as diagnostic markers for the identification of wood of different species, from different islands and regions.

The rapid conversion of Southeast Asian lowland rainforests into monocultures calls for the development of rapid methods for species identification to support ecological research and sustainable land‐use management. Here, we investigated the utilization of DNA barcodes for identifying flowering plants from Sumatra, Indonesia. A total of 1,207 matK barcodes (441 species) and 2,376 rbcL barcodes (750 species) were successfully generated. The barcode effectiveness is assessed using four approaches: (a) comparison between morphological and molecular identification results, (b) best‐close match analysis with TaxonDNA, (c) barcoding gap analysis, and (d) formation of monophyletic groups. Results show that rbcL has a much higher level of sequence recoverability than matK (95% and 66%). The comparison between morphological and molecular identifications revealed that matK and rbcL worked best assigning a plant specimen to the genus level. Estimates of identification success using best‐close match analysis showed that >70% of the investigated species were correctly identified when using single barcode. The use of two‐loci barcodes was able to increase the identification success up to 80%. The barcoding gap analysis revealed that neither matK nor rbcL succeeded to create a clear gap between the intraspecific and interspecific divergences. However, these two barcodes were able to discriminate at least 70% of the species from each other. Fifteen genera and twenty‐one species were found to be nonmonophyletic with both markers. The two‐loci barcodes were sufficient to reconstruct evolutionary relationships among the plant taxa in the study area that are congruent with the broadly accepted APG III phylogeny.

No abstract

Shorea is the largest and most important genus of the Dipterocarpaceae. The genetic diversity and structure of nine Shorea species from two different locations, namely Nanjak Makmur in Sumatra and Sumalindo in Borneo, were evaluated using amplified fragment length polymorphism (AFLP) markers. A total of 274 trees were investigated at 85 polymorphic AFLP loci. Levels of genetic diversity of these species ranged from H e =0.100 for S. acuminata to H e =0.165 for S. blumutensis. The population of rare species S. blumutensis possessed the highest genetic diversity suggesting that geographically restricted species can have levels of genetic variation comparable to closely related widespread common congeners. Analyses of molecular variance revealed that the genetic variation was mainly found among species in both locations (57.7% in Sumatra; 56.3% in Borneo). The unweighted pairgroup method using arithmetic averages dendrogram of all samples revealed an almost complete separation of species. Thus, AFLP markers proved appropriate for phylogenetic studies of Shorea species. Specific markers have been detected showing high-frequency differences among species and between regions within species. Sequence information of these markers can be used to develop specific polymerase chain reaction markers for wood identification. The possibility of interspecific hybridization was discussed.

Genetic differentiation was investigated among 54 Indonesian species of Dipterocarpaceae, a dominant tree family in Asian tropical rainforests, using amplified fragment length polymorphism markers. The tree developed from the resultant unweighted pair group method using arithmetic averages clearly separated all investigated dipterocarps into two major groups that corresponded to tribe Dipterocarpeae and tribe Shoreae, respectively. These results are in accordance with the topology of molecular phylogenetic trees derived from PCR-restriction fragment length polymorphism analysis of chloroplast DNA and generally support the traditional taxonomic assessments. The possibility of interspecific hybridization is also discussed.

Hyperdiverse tropical rainforests, such as the aseasonal forests in Southeast Asia, are supported by high annual rainfall. Its canopy is dominated by the species-rich tree family of Dipterocarpaceae (Asian dipterocarps), which has both ecological (e.g., supports flora and fauna) and economical (e.g., timber production) importance. Recent ecological studies suggested that rare irregular drought events may be an environmental stress and signal for the tropical trees. We assembled the genome of a widespread but near threatened dipterocarp, Shorea leprosula, and analyzed the transcriptome sequences of ten dipterocarp species representing seven genera. Comparative genomic and molecular dating analyses suggested a whole-genome duplication close to the Cretaceous-Paleogene extinction event followed by the diversification of major dipterocarp lineages (i.e. Dipterocarpoideae). Interestingly, the retained duplicated genes were enriched for genes upregulated by no-irrigation treatment. These findings provide molecular support for the relevance of drought for tropical trees despite the lack of an annual dry season.

Melia azedarach L. or mindi (local name) is one of the widely planted exotic species in Indonesia, mostly found in community forests in West Java. However, improving and increasing the productivity of mindi commmunity plantation in West Java requires information on patterns of existing genetic diversity. The present work was aimed at estimating the genetic variation of mindi by using RAPD markers. Outcome of the activities was to propose appropriate conservation and management strategies of genetic resources in order to support the establishment of seed sources. Six populations of mindi plantation in the community forests were chosen for this research, i.e Sukaraja (Bogor-1), Megamendung (Bogor-2), Bandung, Purwakarta, Sumedang and Kuningan. Five primers (OPA-07, OPY-13, OPY-16, OPA-09 and OPO-05) producing reproducible bands were analysed for 120 selected mother trees in total, in which 20 trees per locality were sampled. Data were analysed using Popgene ver 1.31, NTSYS 2.02 and GenAlEx 6.3. Based on the analysis, the observed number of alleles per locus ranging from 1.43 to 1.60, and percentage of polymorphic loci (PPL) ranging from 43.33 to 60.00.%. The levels of genetic variation were considered as moderate for all populations (H e range from 0.1603 to 0.1956) and the the mean level of genetic diversity between population (G st) was 0.3005. Cluster analysis and Principal Coordinates showed three main groups, the first group consists of 4 populations i.e Bandung, Kuningan, Purwakarta and Megamendung, the second was Sukaraja and the third was Sumedang. Based on Analysis of Molecular Variance (AMOVA), the Percentages of Molecular Variance within population (69%) is higher than that of between populations (31%). The moderate level of genetic variation in the community plantation forests, might be due to small population size, leading to reduce genetic variability. Further analysis is required to confirm this findings using other genetic marker.

Mangifera casturi Kosterm., a mango plant from Kalimantan Selatan, Indonesia, has limited genetic information, severely limiting the research on its genetic variation and phylogeny. We collected M. casturi’s genomic information using next-generation sequencing, developed microsatellite markers and performed Sanger sequencing for DNA barcoding analysis. These markers were used to confirm parental origin and genetic diversity of M. casturi hybrids. The clean reads of the Kasturi accession were assembled de novo, producing 259 872 scaffolds (N50 = 1 445 bp). Fourteen polymorphic microsatellite markers were developed from 11 040 microsatellite motif-containing sequences. In total, 58 alleles were produced with a mean of 4.14 alleles per locus. Microsatellite marker analysis revealed broad genetic variation in M. casturi. Phylogenetic analysis was performed using internal transcribed spacers (ITS), matK, rbcL, and trnH-psbA. The phylogenetic tree of chloroplast markers placed Kasturi, Cuban, Pelipisan, Pinari, and Hambawang in one group, with M. indica as the female ancestor. Meanwhile, the phylogenetic tree of ITS markers indicated several Mangifera species as ancestors of M. casturi. Thus, M. casturi very likely originated from the cross-hybridization of multiple ancestors. Furthermore, crossing the F1 hybrids of M. indica and M. quadrifida with other Mangifera spp. may have generated much genetic variation. The genetic information for M. casturi will be a resource for breeding improvement, and conservation studies.