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1. Are the predicted known bacterial strains in a sample really present? A case study

   https://doi.org/10.1371/journal.pone.0291964  

   Ventolero, Minerva; Wang, Saidi; Hu, Haiyan; Li, Xiaoman (October 2023, PLOS ONE)

   El_Allali, Achraf (Ed.)

   With mutations constantly accumulating in bacterial genomes, it is unclear whether the previously identified bacterial strains are really present in an extant sample. To address this question, we did a case study on the known strains of the bacterial speciesS.aureusandS.epidermisin 68 atopic dermatitis shotgun metagenomic samples. We evaluated the likelihood of the presence of all sixteen known strains predicted in the original study and by two popular tools in this study. We found that even with the same tool, only two known strains were predicted by the original study and this study. Moreover, none of the sixteen known strains was likely present in these 68 samples. Our study thus indicates the limitation of the known-strain-based studies, especially those on rapidly evolving bacterial species. It implies the unlikely presence of the previously identified known strains in a current environmental sample. It also called for de novo bacterial strain identification directly from shotgun metagenomic reads. 

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2. The Use of RelocaTE and Unassembled Short Reads to Produce High-Resolution Snapshots of Transposable Element Generated Diversity in Rice

   https://doi.org/10.1534/g3.112.005348  

   Robb, Sofia M; Lu, Lu; Valencia, Elizabeth; Burnette, James M; Okumoto, Yutaka; Wessler, Susan R; Stajich, Jason E (June 2013, G3 Genes|Genomes|Genetics)

   Abstract Transposable elements (TEs) are dynamic components of genomes that often vary in copy number among members of the same species. With the advent of next-generation sequencing TE insertion-site polymorphism can be examined at an unprecedented level of detail when combined with easy-to-use bioinformatics software. Here we report a new tool, RelocaTE, that rapidly identifies specific TE insertions that are either polymorphic or shared between a reference and unassembled next-generation sequencing reads. Furthermore, a novel companion tool, CharacTErizer, exploits the depth of coverage to classify genotypes of nonreference insertions as homozygous, heterozygous or, when analyzing an active TE family, as rare somatic insertion or excision events. It does this by comparing the numbers of RelocaTE aligned reads to reads that map to the same genomic position without the TE. Although RelocaTE and CharacTErizer can be used for any TE, they were developed to analyze the very active mPing element which is undergoing massive amplification in specific strains of Oryza sativa (rice). Three individuals of one of these strains, A123, were resequenced and analyzed for mPing insertion site polymorphisms. The majority of mPing insertions found (~97%) are not present in the reference, and two siblings from a self-crossed of this strain were found to share only ~90% of their insertions. Private insertions are primarily heterozygous but include both homozygous and predicted somatic insertions. The reliability of the predicted genotypes was validated by polymerase chain reaction. 

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3. Overlap detection on long, error-prone sequencing reads via smooth q -gram

   https://doi.org/10.1093/bioinformatics/btaa252  

   Song, Yan; Tang, Haixu; Zhang, Haoyu; Zhang, Qin (April 2020, Bioinformatics)

   Yann, Ponty (Ed.)

   Abstract Motivation Third generation sequencing techniques, such as the Single Molecule Real Time technique from PacBio and the MinION technique from Oxford Nanopore, can generate long, error-prone sequencing reads which pose new challenges for fragment assembly algorithms. In this paper, we study the overlap detection problem for error-prone reads, which is the first and most critical step in the de novo fragment assembly. We observe that all the state-of-the-art methods cannot achieve an ideal accuracy for overlap detection (in terms of relatively low precision and recall) due to the high sequencing error rates, especially when the overlap lengths between reads are relatively short (e.g. <2000 bases). This limitation appears inherent to these algorithms due to their usage of q-gram-based seeds under the seed-extension framework. Results We propose smooth q-gram, a variant of q-gram that captures q-gram pairs within small edit distances and design a novel algorithm for detecting overlapping reads using smooth q-gram-based seeds. We implemented the algorithm and tested it on both PacBio and Nanopore sequencing datasets. Our benchmarking results demonstrated that our algorithm outperforms the existing q-gram-based overlap detection algorithms, especially for reads with relatively short overlapping lengths. Availability and implementation The source code of our implementation in C++ is available at https://github.com/FIGOGO/smoothq. Supplementary information Supplementary data are available at Bioinformatics online. 

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4. Whole-genome sequence and assembly of the Javan gibbon ( Hylobates moloch )

   https://doi.org/10.1093/jhered/esac043  

   Escalona, Merly; VanCampen, Jake; Maurer, Nicholas W.; Haukness, Marina; Okhovat, Mariam; Harris, Robert S.; Watwood, Allison; Hartley, Gabrielle A.; O’Neill, Rachel J.; Medvedev, Paul; et al (September 2022, Journal of Heredity)

   Abstract The Javan gibbon, Hylobates moloch, is an endangered gibbon species restricted to the forest remnants of western and central Java, Indonesia, and one of the rarest of the Hylobatidae family. Hylobatids consist of 4 genera (Holoock, Hylobates, Symphalangus, and Nomascus) that are characterized by different numbers of chromosomes, ranging from 38 to 52. The underlying cause of this karyotype plasticity is not entirely understood, at least in part, due to the limited availability of genomic data. Here we present the first scaffold-level assembly for H. moloch using a combination of whole-genome Illumina short reads, 10X Chromium linked reads, PacBio, and Oxford Nanopore long reads and proximity-ligation data. This Hylobates genome represents a valuable new resource for comparative genomics studies in primates. 

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5. Ultracontinuous Single Haplotype Genome Assemblies for the Domestic Cat ( Felis catus ) and Asian Leopard Cat ( Prionailurus bengalensis )

   https://doi.org/10.1093/jhered/esaa057  

   Bredemeyer, Kevin R; Harris, Andrew J; Li, Gang; Zhao, Le; Foley, Nicole M; Roelke-Parker, Melody; O’Brien, Stephen J; Lyons, Leslie A; Warren, Wesley C; Murphy, William J (December 2020, Journal of Heredity)

   Shapiro, Beth (Ed.)

   Abstract In addition to including one of the most popular companion animals, species from the cat family Felidae serve as a powerful system for genetic analysis of inherited and infectious disease, as well as for the study of phenotypic evolution and speciation. Previous diploid-based genome assemblies for the domestic cat have served as the primary reference for genomic studies within the cat family. However, these versions suffered from poor resolution of complex and highly repetitive regions, with substantial amounts of unplaced sequence that is polymorphic or copy number variable. We sequenced the genome of a female F1 Bengal hybrid cat, the offspring of a domestic cat (Felis catus) x Asian leopard cat (Prionailurus bengalensis) cross, with PacBio long sequence reads and used Illumina sequence reads from the parents to phase >99.9% of the reads into the 2 species’ haplotypes. De novo assembly of the phased reads produced highly continuous haploid genome assemblies for the domestic cat and Asian leopard cat, with contig N50 statistics exceeding 83 Mb for both genomes. Whole-genome alignments reveal the Felis and Prionailurus genomes are colinear, and the cytogenetic differences between the homologous F1 and E4 chromosomes represent a case of centromere repositioning in the absence of a chromosomal inversion. Both assemblies offer significant improvements over the previous domestic cat reference genome, with a 100% increase in contiguity and the capture of the vast majority of chromosome arms in 1 or 2 large contigs. We further demonstrated that comparably accurate F1 haplotype phasing can be achieved with members of the same species when one or both parents of the trio are not available. These novel genome resources will empower studies of feline precision medicine, adaptation, and speciation. 

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