A global-scale screening of non-native aquatic organisms to identify potentially invasive species under current and future climate conditions

The threat posed by invasive non-native species worldwide requires a global approach to identify which introduced species are likely to pose an elevated risk of impact to native species and ecosystems. To inform policy, stakeholders and management decisions on global threats to aquatic ecosystems, 195 assessors representing 120 risk assessment areas across all six inhabited continents screened 819 non-native species from 15 groups of aquatic organisms (freshwater, brackish, marine plants and animals) using the Aquatic Species Invasiveness Screening Kit. This multi-lingual decision-support tool for the risk screening of aquatic organisms provides assessors with risk scores for a species under current and future climate change conditions that, following a statistically based calibration, permits the accurate classification of species into high-, medium-and low-risk categories under current and predicted climate conditions. The 1730 screenings undertaken encompassed wide geographical areas (regions, political entities, parts thereof, water bodies, river basins, lake drainage basins, and marine regions), which permitted thresholds to be identified for almost all aquatic organismal groups screened as well as for tropical, temperate and continental climate classes, and for tropical and temperate marine ecoregions. In total, 33 species were identified as posing a 'very high risk' of being or becoming invasive, and the scores of several of these species under current climate increased under future climate conditions, primarily due to their wide thermal tolerances. The risk thresholds determined for taxonomic groups and climate zones provide a basis against which area-specific or climate-based calibrated thresholds may be interpreted. In turn, the risk rankings help decision-makers identify which species require an immediate 'rapid' management action (e.g. eradication, control) to avoid or mitigate adverse impacts, which require a full risk assessment, and which are to be restricted or banned with regard to importation and/or sale as ornamental or aquarium/fishery enhancement. Decision support tools AS-ISK Hazard identification Non-native species Risk analysis Climate changepublishedVersio

A global-scale screening of non-native aquatic organisms to identify potentially invasive species under current and future climate conditions

The threat posed by invasive non-native species worldwide requires a global approach to identify which introduced species are likely to pose an elevated risk of impact to native species and ecosystems. To inform policy, stakeholders and management decisions on global threats to aquatic ecosystems, 195 assessors representing 120 risk assessment areas across all six inhabited continents screened 819 non-native species from 15 groups of aquatic organisms (freshwater, brackish, marine plants and animals) using the Aquatic Species Invasiveness Screening Kit. This multi-lingual decision-support tool for the risk screening of aquatic organisms provides assessors with risk scores for a species under current and future climate change conditions that, following a statistically based calibration, permits the accurate classification of species into high-, medium- and low-risk categories under current and predicted climate conditions. The 1730 screenings undertaken encompassed wide geographical areas (regions, political entities, parts thereof, water bodies, river basins, lake drainage basins, and marine regions), which permitted thresholds to be identified for almost all aquatic organismal groups screened as well as for tropical, temperate and continental climate classes, and for tropical and temperate marine ecoregions. In total, 33 species were identified as posing a ‘very high risk’ of being or becoming invasive, and the scores of several of these species under current climate increased under future climate conditions, primarily due to their wide thermal tolerances. The risk thresholds determined for taxonomic groups and climate zones provide a basis against which area-specific or climate-based calibrated thresholds may be interpreted. In turn, the risk rankings help decision-makers identify which species require an immediate ‘rapid’ management action (e.g. eradication, control) to avoid or mitigate adverse impacts, which require a full risk assessment, and which are to be restricted or banned with regard to importation and/or sale as ornamental or aquarium/fishery enhancement.publishedVersio

An inexpensive and high-throughput procedure to extract and purify total genomic DNA for population studies

We describe here a procedure for the purification of high molecular weight genomic DNA that combines the economies of ‘do-it-yourself’, single-tube protocols with the sample throughput and DNA quality of microplate-based DNA extraction and purification kits from commercial suppliers. The procedure allows the preparation of genomic DNA of a quality suitable for polymerase chain reaction-based studies of large populations at around one-tenth of the cost of commercially available kits. Furthermore, 96 samples can be purified from crude tissue digests in around 30 min and are produced in microtitre plate format to allow efficient downstream processing of samples

Mining homologues of rice domestication genes in an Australian wild grass species

Extensive sequencing and comparative mapping has established a high degree of conservation between rice and other grasses, allowing the isolation of the corresponding homologues of important rice genes in other grasses. In this study, a number of known rice domestication genes are being used as references to characterize homologues in a wild rice relative, Microlaena stipoides, also known as weeping grass. Whole genome sequence data for M. stipoides was generated by Illumina GAII and assembled by reference to the genome sequence of domesticated rice to generate species specific PCR primers for putative BADH2, GW2 and Hd6 homologues in M. stipoides. Pooled PCR amplicons for these homologues generated from both chemically induced mutant and naturally occurring populations were then screened using the Illumina GAII platform to discover single nucleotide polymorphisms (SNPs). We present a new method of SNPs discovery using the Illumina GAII as a quick and efficient method comparable to Sanger sequencing. We will report the SNPs frequency of putative homologues of BADH2, GW2 and Hd6 in M. stipoides. Potentially useful SNP can be used in establishing new breeding lines of M. stipoides suitable for domestication. Once domesticated, M. stipoides will become a new crop for commercial food production

Mining rice domestication related genes in in Microlaena stipoides

Microlaena stipoides, commonly known as weeping grass, is a distant relative of rice. It is a drought, frost and shade tolerant perennial evergreen plant and produces seeds similar to rice. M. stipoides can be used for grain production and additionally it can be grazed as a pasture. This species responds well to nitrogen application and also regular irrigation, making commercial production possible and making it a target for domestication. Extensive sequencing and comparative mapping has established a high degree of conservation between rice and other grasses, allowing the isolation of the corresponding homologues of important rice genes in other grasses. Whole genome shotgun sequencing has been performed on M. stipoides using Illumina Genome Analyzer IIx. The results have allowed the mining of rice domestication related genes in M. stipoides. This technique has the potential to be utilised for other wild grasses to screen for desirable domestication related traits

Characterising homologues of crop domestication genes in poorly described wild crop relatives by high throughput sequencing of whole genomes

Wild crop relatives represent a source of novel alleles for crop genetic improvement. Screening biodiversity for useful or diverse gene homologues has often been based upon the amplification of targeted genes using available sequence information to design primers that amplify the target gene region across species. The crucial requirement of this approach is the presence of sequences with sufficient conservation across species to allow for the design of universal primers. This approach is often not successful with diverse organisms or highly variable genes. Massively parallel sequencing (MPS) can quickly produce large amounts of sequence data and provides a viable option for characterizing homologues of known genes in poorly described genomes. MPS of genomic DNA was used to obtain species-specific sequence information for 18 rice genes related to domestication characteristics in a wild relative of rice, Microlaena stipoides. Species-specific primers were available for 16 genes compared with 12 genes using the universal primer method. The use of species-specific primers had the potential to cover 92% of the sequence of these genes, while traditional universal primers could only be designed to cover 80%. A total of 24 species-specific primer pairs were used to amplify gene homologues, and 11 primer pairs were successful in capturing six gene homologues. The 23 million, 36-base pair (bp) paired end reads, equated to an average of 2X genome coverage, facilitated the successful amplification and sequencing of six target gene homologues, illustrating an important approach to the discovery of useful genes in wild crop relatives

Whole genome shotgun sequences for microsatellite discovery and application in cultivated and wild Macadamia (Proteaceae)

Premise of the study: Next-generation sequencing (NGS) data are widely used for single-nucleotide polymorphism discovery and genetic marker development in species with limited available genome information. We developed microsatellite primers for the Proteaceae nut crop species Macadamia integrifolia and assessed cross-species transferability in all congeners to investigate genetic identification of cultivars and gene flow. Methods and Results: Primers were designed from both raw and assembled Illumina NGS paired-end reads. The final 12 microsatellite markers selected were polymorphic among wild individuals of all four Macadamia species—M. integrifolia, M. tetraphylla, M. ternifolia,and M. jansenii—and in commercial macadamia cultivars including hybrids. Conclusions: We demonstrate the utility of raw and assembled Illumina NGS reads from total genomic DNA for the rapid development of microsatellites in Macadamia. These primers will facilitate future studies of population structure, hybridization, parentage, and cultivar identification in cultivated and wild Macadamia populations

Utility of mutagenesis and next generation sequencing for accelerating the domestication of a new niche cereal

A native Australian perennial grass has been targeted for accelerated domestication utilising a combination of mutation breeding and high throughput genomics. Ecovars of Microlaena stipoides exhibit high water use efficiency and have demonstrated adaptability to a suite of abiotic stresses including drought, frost, shade, salt and acid soils. Once established, M. stipoides would be maintained as a zero-till crop which produces reasonable yields of grain of similar size, taste, texture and cooking properties as rice. Accelerated domestication primarily targeted the development of a non-shattering phenotype. Ethyl methanesulfonate was used to induce point mutations in a selected breeding line of M. stipoides with the aim of inducing a loss of function at the homologues of the qSH1 and SHA1 shattering loci identified in Oryza sativa. Amplicons of both of these loci were pooled from 109 control samples and compared with a pool of 109 potential mutant samples and a further pool of 754 potential mutants, and screened for single nucleotide polymorphisms (SNP) using next generation sequencing on the Illumina GA II platform. Putatively functional SNP were identified at both homologous loci. Forty-six elite breeding lines, of which 24 were non-shattering at the M2 generation, have been developed and are currently under cultivation for M3 phenotypic screening. It is envisaged that this methodology could be employed to accelerate the domestication of other wild grasses, which have intrinsic abiotic adaptability, as new food, fibre and fuel crops