Article
Biochemical Research Methods
Xiaowen Feng, Haoyu Cheng, Daniel Portik, Heng Li
Summary: hifiasm-meta is a software tool designed for assembling metagenomes using high-accuracy long-read data, which can reconstruct bacterial genomes in microbial communities more accurately.
Article
Biochemical Research Methods
Alaina Shumate, Brandon Wong, Geo Pertea, Mihaela Pertea
Summary: Short-read RNA sequencing and long-read RNA sequencing have their own strengths and weaknesses. The new release of StringTie allows for hybrid-read assembly, combining the strengths of both short and long reads to achieve higher accuracy and faster speed.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Marek Kokot, Adam Gudys, Heng Li, Sebastian Deorowicz
Summary: The cost of maintaining a large amount of data generated by third-generation sequencing has become a significant concern in genomic research. Existing algorithms for compressing long reads have only a slight advantage over general-purpose gzip. In this study, we introduce CoLoRd, an algorithm that can significantly reduce the size of third-generation sequencing data without compromising the accuracy of downstream analyses.
Article
Biotechnology & Applied Microbiology
Guillaume Holley, Doruk Beyter, Helga Ingimundardottir, Peter L. Moller, Snodis Kristmundsdottir, Hannes P. Eggertsson, Bjarni Halldorsson
Summary: Ratatosk is a method presented to correct long reads with short read data, reducing the error rate of long reads 6-fold on average and significantly improving the accuracy of SNP and indel calls. An assembly of Ratatosk corrected reads from an individual showed better contig N50 and less misassemblies compared to a PacBio HiFi reads assembly.
Article
Multidisciplinary Sciences
Mohamed Awad, Xiangchao Gan
Summary: This paper introduces GALA, a computational framework for chromosome-based sequencing data separation and gap-free de novo assembly. It allows integration of different data sources and addresses the challenge of achieving gap-free chromosome-scale assemblies using current workflows for long-read platforms. The method is demonstrated through the assembly of various genomes.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Junwei Luo, Ting Guan, Guolin Chen, Zhonghua Yu, Haixia Zhai, Chaokun Yan, Huimin Luo
Summary: In this article, a hybrid scaffolding method (SLHSD) is introduced that combines the advantages of short reads and long reads to construct an optimal scaffold graph for assembly. Experimental results demonstrate that SLHSD outperforms other methods in terms of performance.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biology
Stephan Schmeing, Mark D. Robinson
Summary: Continuity, correctness, and completeness of genome assemblies are crucial for biological projects. Long reads are beneficial for high-quality genomes, but not everyone can achieve the required coverage. Therefore, improving existing assemblies with low-coverage long reads is a promising alternative, involving correction, scaffolding, and gap filling. We propose a new tool, gapless, which combines all three tasks using PacBio or Oxford Nanopore reads. It can be accessed at https://github.com/schmeing/gapless.
LIFE SCIENCE ALLIANCE
(2023)
Article
Biology
Arne Ludwig, Martin Pippel, Gene Myers, Michael Hiller
Summary: In this study, we present DENTIST, a sensitive, highly accurate, and automated pipeline method for closing gaps in short-read assemblies with long error-prone reads. Through tests on real genomic data, we demonstrate that DENTIST achieves higher accuracy and similar sensitivity compared to previous methods.
Article
Biochemistry & Molecular Biology
Dmitry Meleshko, Rui Yang, Patrick Marks, Stephen Williams, Iman Hajirasouliha
Summary: Recent pan-genome studies have shown that there are many DNA sequences in human genomes that are not present in the reference genome. These non-reference sequences cannot be reliably assembled or placed on the reference genome. In this study, a novel algorithm called Novel-X was proposed to improve the detection of non-reference sequences using barcode information encoded in synthetic long reads. Evaluations showed that Novel-X was able to find many non-reference sequences that could not be detected by state-of-the-art short-read methods.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Lauren Coombe, Janet X. Li, Theodora Lo, Johnathan Wong, Vladimir Nikolic, Rene L. Warren, Inanc Birol
Summary: LongStitch is a scalable pipeline that corrects and scaffolds draft genome assemblies exclusively using long reads. It incorporates multiple tools developed by the group and runs in up to three stages, including initial assembly correction (Tigmint-long), followed by two incremental scaffolding stages (ntLink and ARKS-long). Tested on various organisms and consistently improving assembly contiguity compared to other tools, LongStitch is expected to benefit a wide variety of de novo genome assembly projects.
BMC BIOINFORMATICS
(2021)
Article
Microbiology
McKenna Hicks, Thuy-Khanh Tran-Dao, Logan Mulroney, David L. Bernick
Summary: Limnospira genus, previously classified organisms from Arthrospira commercially marketed as Spirulina, lacks a closed genome and a reference genome for the type strain Limnospira fusiformis. Genome sequencing of L. fusiformis using ultra-long reads resulted in a 6.42 Mb closed genome assembled as a single contig, providing a valuable reference for future biotechnological development. Additionally, a rapid axenicity method was presented for isolating L. fusiformis.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Stephanie H. Chen, Maurizio Rossetto, Marlien van der Merwe, Patricia Lu-Irving, Jia-Yee S. Yap, Herve Sauquet, Greg Bourke, Timothy G. Amos, Jason G. Bragg, Richard J. Edwards
Summary: This study presents the first chromosome-level genome of Telopea speciosissima, providing valuable insights into the speciation, introgression, and adaptation processes. The genome assembly is of high quality and the annotation revealed important genetic information, such as the presence of CYCLOIDEA genes and potential gene duplications. The T. speciosissima reference genome will contribute to the conservation efforts of Proteaceae plants in Australia and beyond.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biochemistry & Molecular Biology
Shunhua Han, Guilherme B. Dias, Preston J. Basting, Raghuvir Viswanatha, Norbert Perrimon, Casey M. Bergman
Summary: Animal cell lines often undergo extreme genome restructuring events that hinder de novo whole-genome assembly. This study used long-read and linked-read technologies to sequence the genome of a tetraploid Drosophila cell line and developed a novel method called TELR for TE analysis. The results shed light on the role and mechanism of transposable elements in animal cell culture genome evolution.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Xiao Luo, Xiongbin Kang, Alexander Schoenhuth
Summary: This article introduces a method based on variation graphs for error correction in long-read sequencing data. This method reduces error correction by using a graph-based reference system, addressing the bias issue caused by consensus sequences in current methods. Extensive benchmarking experiments show that the corrected long reads using this method have 4 to 15 times fewer errors compared to state-of-the-art approaches. Using VeChat prior to long-read assembly also significantly improves haplotype awareness.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Ying Chen, Fan Nie, Shang-Qian Xie, Ying-Feng Zheng, Qi Dai, Thomas Bray, Yao-Xin Wang, Jian-Feng Xing, Zhi-Jian Huang, De-Peng Wang, Li-Juan He, Feng Luo, Jian-Xin Wang, Yi-Zhi Liu, Chuan-Le Xiao
Summary: The error correction and de novo assembly tool NECAT developed by the authors efficiently produces high-quality assemblies of nanopore reads. The tool utilizes adaptive read selection and a two-step progressive method to overcome the high error rates in nanopore reads.
NATURE COMMUNICATIONS
(2021)
Article
Evolutionary Biology
Maiko L. Lutz, Zeb Tonkin, Jian D. L. Yen, Glen Johnson, Brett A. Ingram, Joanne Sharley, Jarod Lyon, David G. Chapple, Paul Sunnucks, Alexandra Pavlova
Summary: By utilizing genetic diversity from different sources, population reintroductions can create populations with low risk of harmful inbreeding and well-equipped for adaptation to future environments. The study assessed the outcomes of reintroducing Macquaria australasica into the Ovens River using genetically diverse Yarra and moderately diverse Dartmouth sources, showing that combining compatible stocks can benefit restoration of wildlife populations.
EVOLUTIONARY APPLICATIONS
(2021)
Review
Ecology
Rebecca E. Koch, Katherine L. Buchanan, Stefania Casagrande, Ondi Crino, Damian K. Dowling, Geoffrey E. Hill, Wendy R. Hood, Matthew McKenzie, Mylene M. Mariette, Daniel W. A. Noble, Alexandra Pavlova, Frank Seebacher, Paul Sunnucks, Eve Udino, Craig R. White, Karine Salin, Antoine Stier
Summary: The critical role that energy turnover plays in understanding variation in performance and fitness among individuals has long been recognized by biologists. While whole-organism metabolic studies have provided key insights into ecological and evolutionary processes, constraints at subcellular levels, such as within mitochondria, can also optimize metabolism. This exploration of mitochondrial aerobic metabolism's influence on organismal performance highlights important areas for future research in understanding ecological and evolutionary processes.
TRENDS IN ECOLOGY & EVOLUTION
(2021)
Article
Ecology
Yael S. Rodger, Alexandra Pavlova, Steve Sinclair, Melinda Pickup, Paul Sunnucks
Summary: Conservation management can be enhanced by understanding genetic diversity and evolutionary history. The Button Wrinklewort daisy has become endangered due to habitat loss and livestock grazing, with genetic analysis showing strong population differentiation between regions. Despite lower recent census sizes, the last two remaining Victorian populations have the highest genetic diversity among the populations studied.
Article
Biochemistry & Molecular Biology
Diana A. Robledo-Ruiz, Alexandra Pavlova, Rohan H. Clarke, Michael J. L. Magrath, Bruce Quin, Katherine A. Harrisson, Han Ming Gan, Gabriel W. Low, Paul Sunnucks
Summary: The article presents an analytical framework for evaluating the efficacy of breeding management strategies for wild populations, showing that the proposed strategies did not significantly improve genetic quality or reduce inbreeding in the critically endangered helmeted honeyeater population. The results demonstrate the usefulness of the analytical framework for testing different in situ breeding strategies and making evidence-based management decisions.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biodiversity Conservation
Joseph P. Zilko, Dan Harley, Alexandra Pavlova, Paul Sunnucks
Summary: Genetic rescue can reduce the extinction risk of inbred populations, with the risk of genetic swamping. Simulation results suggest that translocating highland possums into lowland populations can rapidly increase population size, alleviate inbreeding depression, but may reduce the frequency of locally unique alleles.
Article
Biodiversity Conservation
Anna F. Senior, Nick Clemann, Michael G. Gardner, Katherine A. Harrisson, Geoffrey M. While, David G. Chapple
Summary: The threatened swamp skink (Lissolepis coventryi) has experienced significant habitat loss in the last 150 years, leading to the separation of populations into distinct lineages. Populations in the Melbourne metropolitan area showed signs of limited genetic diversity, likely due to geological and climate influences causing isolation of populations. Management strategies such as translocations, habitat restoration, and protection are important for the conservation of L. coventryi.
CONSERVATION GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Alexandra Pavlova, Katherine A. Harrisson, Rustam Turakulov, Yin Peng Lee, Brett A. Ingram, Dean Gilligan, Paul Sunnucks, Han Ming Gan
Summary: This study identified sex-linked loci in Macquarie perch and developed a cost-effective sexing assay using genomic and resequencing data. The research revealed high instability of sex chromosomes in Percichthyidae fishes, with differences in sex-linked positions observed between species and populations.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biodiversity Conservation
Maiko L. Lutz, Paul Sunnucks, David G. Chapple, Dean Gilligan, Mark Lintermans, Alexandra Pavlova
Summary: This study assessed the genetic outcomes of interbreeding between two lineages of a threatened freshwater fish species, and found no adverse effects from genetic mixing of populations separated by over 100,000 years.
CONSERVATION GENETICS
(2022)
Article
Biodiversity Conservation
Alexandra Pavlova, Sara Petrovic, Katherine A. Harrisson, Karina Cartwright, Elizabeth Dobson, Laura L. Hurley, Meagan Lane, Michael J. L. Magrath, Kimberly A. Miller, Bruce Quin, Monique Winterhoff, Jian D. L. Yen, Paul Sunnucks
Summary: Small, isolated populations face the risk of extinction due to inbreeding depression, loss of beneficial variation, and reduced adaptability. Genetic rescue through gene flow from diverse sources is the most effective way to improve their fitness. However, the use of a different subspecies as a potential source of immigrants may result in reduced fitness of mixed offspring. Test cases are necessary to evaluate and manage such risky rescues.
BIOLOGICAL CONSERVATION
(2023)
Article
Biochemistry & Molecular Biology
Diana A. Robledo-Ruiz, Lana Austin, J. Nevil Amos, Jesus Castrejon-Figueroa, Daniel K. P. Harley, Michael J. L. Magrath, Paul Sunnucks, Alexandra Pavlova
Summary: Identifying sex-linked markers in genomic datasets is crucial for accurate genetic analysis and interpretation. However, current methods often neglect certain types of sex-linked variation. In this study, we developed new R functions that can reliably identify sex-linked loci and infer the genetic sex of individuals. We tested these functions on bird and mammal species and found that they achieved high accuracy in distinguishing sex-linked loci from autosomal loci. Furthermore, we demonstrated that failure to remove sex-linked loci can lead to incorrect biological inferences and management recommendations. Our functions provide a convenient tool for removing sex-linked loci in reduced-representation datasets and sexing individuals.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Fisheries
J. E. O'Dwyer, N. Murphy, Z. Tonkin, J. Lyon, W. Koster, D. Dawson, F. Amtstaetter, K. A. Harrisson
Summary: The study found differences in genetic connectivity among three diadromous Australian fish species, with common galaxias being highly connected while Australian grayling and tupong showed patterns of isolation by distance. The genetic connectivity of tupong and Australian grayling appeared to be unrelated to oceanic currents, highlighting the potential value of genetic tools in informing species-specific management plans.
MARINE AND FRESHWATER RESEARCH
(2021)
Article
Ornithology
James Q. Radford, Nevil Amos, Katherine Harrisson, Paul Sunnucks, Alexandra Pavlova
Summary: This review article highlights the impact of habitat loss and fragmentation on population adaptation, as well as the finding that high genetic connectivity does not necessarily indicate healthy populations. The study conducted on woodland bird species in central Victoria, Australia provides valuable insights for conservation management strategies.
EMU-AUSTRAL ORNITHOLOGY
(2021)
