Genome sequencing: a grin without a cat

In some types of unicellular algae, the chloroplasts have their own nucleus — a legacy of the time when the chloroplast was a free-living cell. The sequence of the genome in one such nucleus is now revealed.

Eulerian superpath approach to correct sequencing error in shotgun assembly

This work describes an error correction method based on the Euler Superpath problem. Sequence data is mapped to an Euler Superpath dynamically by Merging Transformation. With restriction and guiding rules, data consistency is maintained and error paths are separated from correct data: Error edges are mapped to the correct ones and after substitution (of error edges with right paths), corresponding errors in the sequencing data are eliminated.

Modeling a just-in-time plant using sequencing algorithms

An Australian automotive component company plans to assemble and deliver seats to customer on just-in-time basis. The company management has decided to model operations of the seat plant to help them make decisions on capital investment and labour requirements. There are four different areas in seat assembly and delivery areas. Each area is modeled independently to optimise its operations. All four areas are then combined into one model called the plant model to model operations of seat plant from assembly to delivery. Discrete event simulation software is used to model the assembly operations of seat plant.

Ecological niche modelling and DNA sequencing support a new, morphologically cryptic beetle species unveiled by DNA barcoding

Background: DNA sequencing techniques used to estimate biodiversity, such as DNA barcoding, may reveal cryptic species. However, disagreements between barcoding and morphological data have already led to controversy. Species delimitation should therefore not be based on mtDNA alone. Here, we explore the use of nDNA and bioclimatic modelling in a new species of aquatic beetle revealed by mtDNA sequence data.

Methodology/Principal Findings: The aquatic beetle fauna of Australia is characterised by high degrees of endemism, including local radiations such as the genus Antiporus. Antiporus femoralis was previously considered to exist in two disjunct, but morphologically indistinguishable populations in south-western and south-eastern Australia. We constructed a phylogeny of Antiporus and detected a deep split between these populations. Diagnostic characters from the highly variable nuclear protein encoding arginine kinase gene confirmed the presence of two isolated populations. We then used ecological niche modelling to examine the climatic niche characteristics of the two populations. All results support the status of the two populations as distinct species. We describe the south-western species as Antiporus occidentalis sp.n.

Conclusion/Significance: In addition to nDNA sequence data and extended use of mitochondrial sequences, ecological niche modelling has great potential for delineating morphologically cryptic species. © 2011 Hawlitschek et al.

The development of 20 microsatellite loci for the Australian marine mollusk, Donax deltoides, through next generation DNA sequencing

 Next Generation DNA sequencing was used to develop a suite of microsatellite markers for the marine mollusk, Donax deltoides. A total of 20 polymorphic loci were identified and 12 characterized using 30 individuals from a single population (Venus Bay) in south eastern Australia. We observed moderate to high genetic variation across most loci (mean number of alleles per locus = 7.3; mean heterozygosity = 0.633) with only a single locus (Ddel32) displaying significant deviation from Hardy–Weinberg equilibrium. Marker independence was confirmed with tests for linkage disequilibrium, however two loci were found to be influenced by null alleles. The 10 viable markers characterized in the present study provide a valuable resource for future population genetic assessments and fisheries management of D. deltoides in Australia.

Development of twenty-four novel microsatellite markers for the freshwater crayfish, Geocharax gracilis, using next generation sequencing

The crayfish Geocharax gracilis is an important inhabitant of natural and agricultural drainage systems in south-eastern Australia. To investigate population structure, genetic diversity and patterns of connectivity in natural and human-altered ecosystems, we isolated and characterised 24 microsatellite loci using next generation sequencing. Loci were initially tested for levels of variation based on 12 individuals from across the species’ geographical range. A further 33 individuals from a single population were used to test for departures from Hardy–Weinberg equilibrium and linkage disequilibrium. We detected high to moderate levels of genetic variation across most loci with a mean allelic richness of 8.42 and observed heterozygosity of 0.629 (all samples combined). We found no evidence for linkage disequilibrium between any loci and only three loci (Geo01, Geo24 and Geo47) showed significant deviations from Hardy–Weinberg expectations. These same three loci, plus two additional loci (Geo06 and Geo28), also showed the presence of null alleles. These 24 variable markers will provide an important tool for future population genetic assessments in natural and human altered environments.

Isolation and characterisation via 454 sequencing of microsatellites from the tawny frogmouth, Podargus strigoides (Class Aves, Family Podargidae)

We isolated 24 novel polymorphic microsatellite markers from the tawny frogmouth, a nocturnal bird endemic to Australia, which has successfully adapted to urban environments. Initially, 454 shotgun sequencing was used to identify 733 loci with primers designed. Of these, we trialled 30 in the target species of which all amplified a product of expected size. Subsequently, all 30 of these loci were screened for variation in 25 individuals, from a single population in Melbourne, Victoria, Australia. Twenty-eight loci were polymorphic with observed heterozygosity ranging from 0.03 to 0.96 (mean 0.58) and the number of alleles per locus ranged from 2 to 18 (average of 6.5); we confirmed that 24 loci conformed to Hardy–Weinberg expectations. The 24 loci identified here will be sufficient to unequivocally identify individuals and will be useful in understanding the reproductive ecology, population genetics and the gene flow amongst localities in urban environments where this bird thrives.