Genome Research

Journal: Genome Research

Abbreviation

Genome Res.

Publisher

Cold Spring Harbor Laboratory Press

ISSN

1088-9051
1549-5469

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Publications 1 - 10 of 30

OMA standalone: orthology inference among public and custom genomes and transcriptomes
Altenhoff, Adrian M.; Levy, Jeremy; Zarowiecki, Magdalena; et al. (2019)
Genome Research
Genomes and transcriptomes are now typically sequenced by individual laboratories but analyzing them often remains challenging. One essential step in many analyses lies in identifying orthologs—corresponding genes across multiple species—but this is far from trivial. The Orthologous MAtrix (OMA) database is a leading resource for identifying orthologs among publicly available, complete genomes. Here, we describe the OMA pipeline available as a standalone program for Linux and Mac. When run on a cluster, it has native support for the LSF, SGE, PBS Pro, and Slurm job schedulers and can scale up to thousands of parallel processes. Another key feature of OMA standalone is that users can combine their own data with existing public data by exporting genomes and precomputed alignments from the OMA database, which currently contains over 2100 complete genomes. We compare OMA standalone to other methods in the context of phylogenetic tree inference, by inferring a phylogeny of Lophotrochozoa, a challenging clade within the protostomes. We also discuss other potential applications of OMA standalone, including identifying gene families having undergone duplications/losses in specific clades, and identifying potential drug targets in nonmodel organisms. OMA standalone is available under the permissive open source Mozilla Public License Version 2.0.
Heterogeneous and novel transcript expression in single cells of patient-derived clear cell renal cell carcinoma organoids
Karakulak, Tülay; Zajac, Natalia; Bolck, Hella Anna; et al. (2025)
Genome Research
Splicing is often dysregulated in cancer, leading to alterations in the expression of canonical and alternatively spliced isoforms. We used the multiplexed arrays sequencing (MAS-seq) protocol of PacBio to sequence full-length transcripts in patient-derived organoid (PDO) cells of clear cell renal cell carcinoma (ccRCC). The sequencing revealed a heterogeneous dysregulation of splicing across 2599 single ccRCC cells. The majority of novel transcripts could be removed with stringent filtering criteria. The remaining 31,531 transcripts (36.6% of the 86,182 detected transcripts on average) were previously uncharacterized. In contrast to known transcripts, many of the novel transcripts have cell-specific expression. Novel transcripts common to ccRCC cells belong to genes involved in ccRCC-related pathways, such as hypoxia and oxidative phosphorylation. A novel transcript of the ccRCC-related gene nicotinamide N-methyltransferase is validated using PCR. Moreover, >50% of novel transcripts possess a predicted complete protein-coding open reading frame. An analysis of the most dominant transcript-switching events between ccRCC and non-ccRCC cells shows many switching events that are cell- and sample-specific, underscoring the heterogeneity of alternative splicing events in ccRCC. Overall, our study elucidates the intricate transcriptomic architecture of ccRCC, underlying its aggressive phenotype and providing insights into its molecular complexity.
Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle
Milia, Sotiria; Leonard, Alexander; Mapel, Xena Marie; et al. (2025)
Genome Research
Cattle have been selectively bred for coat color, spotting, and depigmentation patterns. The assumed autosomal dominant inherited genetic variants underlying the characteristic white head of Fleckvieh, Simmental, and Hereford cattle have not been identified yet, although the contribution of structural variation upstream the KIT gene has been proposed. Here, we construct a graph pangenome from 24 haplotype assemblies representing seven taurine cattle breeds to identify and characterize the white head-associated locus for the first time based on long-read sequencing data and pangenome analyses. We introduce a pangenome-wide association mapping approach which examines assembly path similarities within the graph to reveal an association between two most likely serial alleles of a complex structural variant 66 kb upstream KIT and facial depigmentation. The complex structural variant contains a variable number of tandemly duplicated 14.3 kb repeats, consisting of LTRs, LINEs, and other repetitive elements, leading to misleading alignments of short and long reads when using a linear reference. We align 250 short-read sequencing samples spanning 15 cattle breeds to the pangenome graph, further validating that the alleles of the structural variant segregate with head depigmentation. We estimate an increased count of repeats in Hereford relative to Simmental and other white-headed cattle breeds from the graph alignment coverage, suggesting a large under-assembly in the current Hereford-based cattle reference genome which had fewer copies. Our work shows that exploiting assembly path similarities within graph pangenomes can reveal trait-associated complex structural variants.
A genome-wide transcriptome and translatome analysis of Arabidopsis transposons identifies a unique and conserved genome expression strategy for Ty1/Copia retroelements.
Oberlin, Stefan; Sarazin, Alexis; Chevalier, Clément; et al. (2017)
Genome Research
Pronounced inter- and intrachromosomal variation in linkage disequilibrium across the zebra finch genome
Stapley, Jessica; Birkhead, Tim R.; Burke, Terry; et al. (2010)
Genome Research
mGene
Schweiker,t Gabriele; Zien, Alexander; Zeller, Georg; et al. (2009)
Genome Research
Genomic basis of endosymbiont conferred protection against an insect parasitoid
Hansen, Allison K.; Vorburger, Christoph; Moran, Nancy A. (2012)
Genome Research
Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function
Grobei, Monica A.; Qeli, Ermir; Brunner, Erich; et al. (2009)
Genome Research
Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution
Qin, Qian; Popic, Victoria; Wienand, Kirsty; et al. (2025)
Genome Research
Gene fusions are found as cancer drivers in diverse adult and pediatric cancers. Accurate detection of fusion transcripts is essential in cancer clinical diagnostics and prognostics and for guiding therapeutic development. Most currently available methods for fusion transcript detection are compatible with Illumina RNA-seq involving highly accurate short-read sequences. Recent advances in long-read isoform sequencing enable the detection of fusion transcripts at unprecedented resolution in bulk and single-cell samples. Here, we developed a new computational tool, CTAT-LR-Fusion, to detect fusion transcripts from long-read RNA-seq with or without companion short reads, with applications to bulk or single-cell transcriptomes. We demonstrate that CTAT-LR-Fusion exceeds the fusion detection accuracy of alternative methods as benchmarked with simulated and genuine long-read RNA-seq. Using short- and long-read RNA-seq, we further apply CTAT-LR-Fusion to bulk transcriptomes of nine tumor cell lines and to tumor single cells derived from a melanoma sample and three metastatic high-grade serous ovarian carcinoma samples. In both bulk and single-cell RNA-seq, long isoform reads yield higher sensitivity for fusion detection than short reads with notable exceptions. By combining short and long reads in CTAT-LR-Fusion, we are able to further maximize the detection of fusion splicing isoforms and fusion-expressing tumor cells.
Metabolic functions of duplicate genes in Saccharomyces cerevisiae
Kuepfer, Lars; Sauer, Uwe; Blank, Lars M. (2005)
Genome Research

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