Building a Plant DNA Barcode Reference Library for a Diverse Tropical Flora: An Example from Queensland, Australia

Abstract

A foundation for a DNA barcode reference library for the tropical plants of Australia is presented here. A total of 1572 DNA barcode sequences are compiled from 848 tropical Queensland species. The dataset represents 35% of the total flora of Queensland's Wet Tropics Bioregion, 57% of its tree species and 28% of the shrub species. For approximately half of the sampled species, we investigated the occurrence of infraspecific molecular variation in DNA barcode loci rbcLa, matK, and the trnH-psbA intergenic spacer region across previously recognized biogeographic barriers. We found preliminary support for the notion that DNA barcode reference libraries can be used as a tool for inferring biogeographic patterns at regional scales. It is expected that this dataset will find applications in taxonomic, ecological, and applied conservation research.

Potential DNA barcodes for Melilotus species based on five single loci and their combinations

“…Besides, DNA barcodes were used to identify set of taxa characteristic for a certain region and analyzed as “local flora”. Costion and colleagues employed three types of barcodes ( rbc La, mat K and trn H- psb A) to produce a DNA barcode reference library for Australian tropical plants [ 17 ]. Inter-phylogenetic information and evolutionary history of trees in Puerto Rico were obtained using three DNA barcodes ( rbc L, mat K and trn H -psb A) [ 18 ].…”

Congruent biogeographical disjunctions at a continent-wide scale: Quantifying and clarifying the role of biogeographic barriers in the Australian tropics

“…[90] found genetic divergence in multiple plant species across three barriers in the Australian Wet Tropics: 5 of 19 species across the Burdekin Basin, 37 of 110 species across the Black Mountain Corridor, and 13 of 53 species across the Normanby Basin. This indicates that some level of disruption to gene flow occurs in the vicinity of the barriers but, at this stage, it is not possible to distinguish whether these are abrupt disjunctions or the results of clinal variation [90]. Comparative analyses using molecular data within and among plant species across Australian Monsoon Tropics are clearly needed to assess the role of barriers in structuring plant populations.…”

Herbarium genomics: skimming and plastomics from archival specimens

“…To date, few plant and fungal herbarium DNA barcoding projects have been undertaken however (e.g. Osmundson et al 2013;Costion et al 2016;Do and Drábková 2016;Enan et al 2017) indicating that either PCR challenges or massive parallel sequencing approaches (as in Bakker et al 2016) still need further development. Bebber et al (2010) estimated that around 70,000 new species are already in herbarium collections, "waiting to be described" further underlining the notion that it is time to exploit and mine our herbarium collections genomically, especially with regards to plastomes (but see Gutaker and Burbano 2017), as these probably represent the most feasible and standardizable targets.…”