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Resource: Chromosome-level subgenome-aware de novo assembly provides insight into Saccharomyces bayanus genome divergence after hybridization
- Cory Gardner,
- Junhao Chen,
- Christina Hadfield,
- Zhaolian Lu,
- David Debruin,
- Yu Zhan,
- Maureen J. Donlin,
- Tae-Hyuk Ahn,
- and Zhenguo Lin
Genome Res. November 2024 34: 2133-2146; Published in Advance September 17, 2024, doi:10.1101/gr.279364.124
...these questions as most duplicate genes have been lost. In addition to the ancient hybridization event, recent interspecific hybridization is prevalent in the Saccharomyces lineage as they are used to produce fermented beverages (Langdon et al. 2019). The s of these recently generated hybrids may serve as ideal...
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Method: Single-cell Rapid Capture Hybridization sequencing reliably detects isoform usage and coding mutations in targeted genes
- Hongke Peng,
- Jafar S. Jabbari,
- Luyi Tian,
- Changqing Wang,
- Yupei You,
- Chong Chyn Chua,
- Natasha S. Anstee,
- Noorul Amin,
- Andrew H. Wei,
- Nadia M. Davidson,
- Andrew W. Roberts,
- David C.S. Huang,
- Matthew E. Ritchie,
- and Rachel Thijssen
Genome Res. April 2025 35: 942-955; Published in Advance January 10, 2025, doi:10.1101/gr.279322.124
...expression and 10x Genomics multiome combines transcriptome with chromatin accessibility data (Stoeckius et al. 2017). Our single-cell Rapid Capture Hybridization sequencing (scRaCH-seq) method enables the capture of multiple transcripts from preindexed and stored cDNA independent of the 10x Genomics kit...
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Research: Long-read DNA and cDNA sequencing identify cancer-predisposing deep intronic variation in tumor-suppressor genes
- Suleyman Gulsuner,
- Amal AbuRayyan,
- Jessica B. Mandell,
- Ming K. Lee,
- Greta V. Bernier,
- Barbara M. Norquist,
- Sarah B. Pierce,
- Mary-Claire King,
- and Tom Walsh
Genome Res. November 2024 34: 1825-1831; Published in Advance September 13, 2024, doi:10.1101/gr.279158.124
...their inherent features and from challenges in these early days of their development and rapid application. Most critically, long-read genomic sequencing depends on high-quality DNA, and long-read cDNA sequencing depends on high-quality RNA. These requirements will not change; as in the early days...
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Research: Reactivation of transposable elements following hybridization in fission yeast
- Sergio Tusso,
- Fang Suo,
- Yue Liang,
- Li-Lin Du,
- and Jochen B.W. Wolf
Genome Res. February 2022 32: 324-336; Published in Advance December 14, 2021, doi:10.1101/gr.276056.121
...families. These results are consistent with full-length elements being mostly of young age and solo LTRs being of much older origin.In the S. pombe reference strain, ∼70% of Tf2 mobilization events involve homologous recombination between newly synthesized cDNA and a pre-existing copy of Tf2; the remaining...
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Resource: MPRAbase a Massively Parallel Reporter Assay database
- Jingjing Zhao,
- Fotis A Baltoumas,
- Maxwell A Konnaris,
- Ioannis Mouratidis,
- Zhe Liu,
- Jasmine Sims,
- Vikram Agarwal,
- Georgios A Pavlopoulos,
- Ilias Georgakopoulos-Soares,
- and Nadav Ahituv
Genome Res. April 22, 2025 gr.280387.124; Published in Advance April 22, 2025, doi:10.1101/gr.280387.124
...MPRAbase A Massively Parallel Reporter Assay database Jingjing Zhao1,2,*, Fotis A. Baltoumas3,*, Maxwell A. Konnaris4,5, Ioannis Mouratidis4, Zhe Liu1,2,6, Jasmine Sims1,2, Vikram Agarwal7, Georgios A. Pavlopoulos3, Ilias Georgakopoulos-Soares4,♱, Nadav Ahituv1,2,♱ 1Department of Bioengineering...
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Research: Hybridization drives mitochondrial DNA degeneration and metabolic shift in a species with biparental mitochondrial inheritance
- Mathieu Hénault,
- Souhir Marsit,
- Guillaume Charron,
- and Christian R. Landry
Genome Res. November/December 2022 32: 2043-2056; Published in Advance November 9, 2022, doi:10.1101/gr.276885.122
...A, SpB, and SpC) and Saccharomyces cerevisiae (two strains) (Fig. 1A). Using these parental backgrounds, we designed 11 crosses spanning a range of evolutionary divergence from intra-lineage to interspecific. Each cross was replicated 48 to 96 times with independent matings, totalling 864 hybrid MA...
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Method: Theoretical framework for the difference of two negative binomial distributions and its application in comparative analysis of sequencing data
- Alicia Petrany,
- Ruoyu Chen,
- Shaoqiang Zhang,
- and Yong Chen
Genome Res. October 2024 34: 1636-1650; Published in Advance October 15, 2024, doi:10.1101/gr.278843.123
...properties. As a state-of-the-art application of DOTNB, we introduce DEGage, a computational method for detecting differentially expressed genes (DEGs) in scRNA-seq data. DEGage calculates the mean of the sample-wise differences of gene expression levels as the test statistic and determines significant...
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Method: Complete characterization of the human immune cell transcriptome using accurate full-length cDNA sequencing
- Charles Cole,
- Ashley Byrne,
- Matthew Adams,
- Roger Volden,
- and Christopher Vollmers
Genome Res. April 2020 30: 589-601; Published in Advance April 20, 2020, doi:10.1101/gr.257188.119
...(Volden et al. 2018) or tagmented it with Tn5 to generate a hybrid Smart-seq2 and R2C2 short-read library we named Smar2C2 (Fig. 1). Because of their distinct features, the different libraries were intended for different tasks. R2C2 data were intended to provide full-length cDNA sequences for isoform...
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Methods: Survey of allelic expression using EST mining
- Bing Ge,
- Scott Gurd,
- Tiffany Gaudin,
- Carole Dore,
- Pierre Lepage,
- Eef Harmsen,
- Thomas J. Hudson,
- and Tomi Pastinen
Genome Res. November 2005 15: 1584-1591; doi:10.1101/gr.4023805
...that an SNP is valid, and only SNPs showing evidence of transmission in Caucasian HapMap trios were further studied. Because each cDNA library can maximally contribute two alleles in the EST allele counts, we randomly selected a maximum of two sequences from each library. This reduces the sampling bias...
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Research: Plasma cell-free RNA characteristics in COVID-19 patients
- Yanqun Wang,
- Jie Li,
- Lu Zhang,
- Hai-Xi Sun,
- Zhaoyong Zhang,
- Jinjin Xu,
- Yonghao Xu,
- Yu Lin,
- Airu Zhu,
- Yuxue Luo,
- Haibo Zhou,
- Yan Wu,
- Shanwen Lin,
- Yuzhe Sun,
- Fei Xiao,
- Ruiying Chen,
- Liyan Wen,
- Wei Chen,
- Fang Li,
- Rijing Ou,
- Yanjun Zhang,
- Tingyou Kuo,
- Yuming Li,
- Lingguo Li,
- Jing Sun,
- Kun Sun,
- Zhen Zhuang,
- Haorong Lu,
- Zhao Chen,
- Guoqiang Mai,
- Jianfen Zhuo,
- Puyi Qian,
- Jiayu Chen,
- Huanming Yang,
- Jian Wang,
- Xun Xu,
- Nanshan Zhong,
- Jingxian Zhao,
- Junhua Li,
- Jincun Zhao,
- and Xin Jin
Genome Res. February 2022 32: 228-241; Published in Advance January 21, 2022, doi:10.1101/gr.276175.121
...status.At present, advanced omics research has revealed different perspectives of COVID-19 (Alonso and Diambra 2020; Hughes et al. 2020; Massey et al. 2020; Shen et al. 2020; Zhu et al. 2020a). For instance, one study unveiled characteristic protein and metabolite changes in the sera of severe COVID-19...
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