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Research: Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by resequencing Landsberg erecta and all four products of a single meiosis
- Pingli Lu,
- Xinwei Han,
- Ji Qi,
- Jiange Yang,
- Asela J. Wijeratne,
- Tao Li,
- and Hong Ma
Genome Res. March 2012 22: 508-518; Published in Advance November 21, 2011, doi:10.1101/gr.127522.111
...Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by resequencing Landsberg erecta and all four products of a single meiosis Pingli Lu 1 , 7 , Xinwei Han 1 , 2 , 7 , Ji Qi 3 , 4 , 7 , Jiange Yang...
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RESOURCE: Sequencing of natural strains of Arabidopsis thaliana with short reads
- Stephan Ossowski,
- Korbinian Schneeberger,
- Richard M. Clark,
- Christa Lanz,
- Norman Warthmann,
- and Detlef Weigel
Genome Res. December 2008 18: 2024-2033; Published in Advance September 25, 2008, doi:10.1101/gr.080200.108
...or deleted relative to the reference. To detect such polymorphic regions (PRs), we identified tracts of at least eight contiguous nonrepetitive or moderately repetitive positions covered by one or no read. Because of reduced read coverage for GC-poor regions, we made predictions only when GC content within...
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Resource: A SNP discovery method to assess variant allele probability from next-generation resequencing data
- Yufeng Shen,
- Zhengzheng Wan,
- Cristian Coarfa,
- Rafal Drabek,
- Lei Chen,
- Elizabeth A. Ostrowski,
- Yue Liu,
- George M. Weinstock,
- David A. Wheeler,
- Richard A. Gibbs,
- and Fuli Yu
Genome Res. February 2010 20: 273-280; Published in Advance December 17, 2009, doi:10.1101/gr.096388.109
...-nucleotide polymorphism discovery. Nat Genet 23: 452–456. Ossowski S, Schneeberger K, Clark RM, Lanz C, Warthmann N, Weigel D. 2008. Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res 18: 2024–2033. Quinlan AR, Stewart DA, Stromberg MP, Marth GT. 2008. Pyrobayes: An improved base caller...
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METHODS: Rapid Mapping of Zebrafish Mutations With SNPs and Oligonucleotide Microarrays
- Heather L. Stickney,
- Jeremy Schmutz,
- Ian G. Woods,
- Caleb C. Holtzer,
- Mark C. Dickson,
- Peter D. Kelly,
- Richard M. Myers,
- and William S. Talbot
Genome Res. December 1, 2002 12: 1929-1934; doi:10.1101/gr.777302
...in the region (e.g., mapped SNPs or SSLPs) on individuals. Analysis of pooled samples with the microarray can detect linkage of markers 10–20 cM from the mutation (Figs. 3 and 4 ; data not shown). This indicates that, under ideal conditions, analysis of only 60–120 polymorphic SNPs spaced at intervals of 20...
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METHODS: A System for Specific, High-throughput Genotyping by Allele-specific Primer Extension on Microarrays
- Tomi Pastinen,
- Mirja Raitio,
- Katarina Lindroos,
- Päivi Tainola,
- Leena Peltonen,
- and Ann-Christine Syvänen
Genome Res. July 1, 2000 10: 1031-1042; doi:10.1101/gr.10.7.1031
...because no carrier samples were available. In a recent study, a map comprising 412 SNPs in Arabidopsis thaliana was analyzed using high-density, ASO-based microarrays carrying 72,500 probes, corresponding to 176 probes per SNP, and the correct genotype was assigned for as little as 57% of the analyzed...
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Research: Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control
- Todd P. Michael,
- Evan Ernst,
- Nolan Hartwick,
- Philomena Chu,
- Douglas Bryant,
- Sarah Gilbert,
- Stefan Ortleb,
- Erin L. Baggs,
- K. Sowjanya Sree,
- Klaus J. Appenroth,
- Joerg Fuchs,
- Florian Jupe,
- Justin P. Sandoval,
- Ksenia V. Krasileva,
- Ljudmylla Borisjuk,
- Todd C. Mockler,
- Joseph R. Ecker,
- Robert A. Martienssen,
- and Eric Lam
Genome Res. February 2021 31: 225-238; Published in Advance December 23, 2020, doi:10.1101/gr.266429.120
...; Ferrari et al. 2019). In the model plant Arabidopsis thaliana, as much as 90% of its genes are expressed, or phased, to a specific TOD to optimize growth, and this global transcriptional regulation is conserved across higher plants (Michael et al. 2008a,b; Filichkin et al. 2011). Because Wolffia...
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Resource: Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies
- Mingzhou Li,
- Lei Chen,
- Shilin Tian,
- Yu Lin,
- Qianzi Tang,
- Xuming Zhou,
- Diyan Li,
- Carol K.L. Yeung,
- Tiandong Che,
- Long Jin,
- Yuhua Fu,
- Jideng Ma,
- Xun Wang,
- Anan Jiang,
- Jing Lan,
- Qi Pan,
- Yingkai Liu,
- Zonggang Luo,
- Zongyi Guo,
- Haifeng Liu,
- Li Zhu,
- Surong Shuai,
- Guoqing Tang,
- Jiugang Zhao,
- Yanzhi Jiang,
- Lin Bai,
- Shunhua Zhang,
- Miaomiao Mai,
- Changchun Li,
- Dawei Wang,
- Yiren Gu,
- Guosong Wang,
- Hongfeng Lu,
- Yan Li,
- Haihao Zhu,
- Zongwen Li,
- Ming Li,
- Vadim N. Gladyshev,
- Zhi Jiang,
- Shuhong Zhao,
- Jinyong Wang,
- Ruiqiang Li,
- and Xuewei Li
Genome Res. May 2017 27: 865-874; Published in Advance September 19, 2016, doi:10.1101/gr.207456.116
...of plants (coccolithophores [Read et al. 2013],Arabidopsis thaliana [Gan et al. 2011], soybean [Li et al. 2014], and rice [Zhang et al. 2014]), animals (mosquitoes [Neafsey et al. 2015] and macaques [Yan et al. 2011]), and even modern humans (Li et al. 2010a), a surprisingly large amount of variation has...
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Method: A reduced representation approach to population genetic analyses and applications to human evolution
- Francesca Luca,
- Richard R. Hudson,
- David B. Witonsky,
- and Anna Di Rienzo
Genome Res. July 2011 21: 1087-1098; Published in Advance May 31, 2011, doi:10.1101/gr.119792.110
...to restriction fragments in the range 40–100 bp for the samples in this study. (B) Autosomal regions are evenly represented in the resequencing target and no apparent bias is detected in the genomic distribution of coverage depth (vertical axis). (C ) The plot shows the distribution of %G + C content...
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LETTER: Dynamic evolution at pericentromeres
- Anne E. Hall,
- Gregory C. Kettler,
- and Daphne Preuss
Genome Res. March 2006 16: 355-364; Published in Advance February 6, 2006, doi:10.1101/gr.4399206
...of duplicated and novel genes; in peri- CEN3 , these occur at a surprisingly high frequency: 1 gene/20 kb within 5–10 Myr. View this table: In this window In a new window Table 3. Regions with sequence similarity to A. thaliana genes and hypothetical proteins Similar, but less numerous events were detected...
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Resource: Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines
- Wen Huang,
- Andreas Massouras,
- Yutaka Inoue,
- Jason Peiffer,
- Miquel Ràmia,
- Aaron M. Tarone,
- Lavanya Turlapati,
- Thomas Zichner,
- Dianhui Zhu,
- Richard F. Lyman,
- Michael M. Magwire,
- Kerstin Blankenburg,
- Mary Anna Carbone,
- Kyle Chang,
- Lisa L. Ellis,
- Sonia Fernandez,
- Yi Han,
- Gareth Highnam,
- Carl E. Hjelmen,
- John R. Jack,
- Mehwish Javaid,
- Joy Jayaseelan,
- Divya Kalra,
- Sandy Lee,
- Lora Lewis,
- Mala Munidasa,
- Fiona Ongeri,
- Shohba Patel,
- Lora Perales,
- Agapito Perez,
- LingLing Pu,
- Stephanie M. Rollmann,
- Robert Ruth,
- Nehad Saada,
- Crystal Warner,
- Aneisa Williams,
- Yuan-Qing Wu,
- Akihiko Yamamoto,
- Yiqing Zhang,
- Yiming Zhu,
- Robert R.H. Anholt,
- Jan O. Korbel,
- David Mittelman,
- Donna M. Muzny,
- Richard A. Gibbs,
- Antonio Barbadilla,
- J. Spencer Johnston,
- Eric A. Stone,
- Stephen Richards,
- Bart Deplancke,
- and Trudy F.C. Mackay
Genome Res. July 2014 24: 1193-1208; Published in Advance April 8, 2014, doi:10.1101/gr.171546.113
...deleterious alleles that are closely linked in repulsion. If complementary deleterious alleles are embedded in polymorphic genetically divergent inversions, inversion heterozygotes may be polymorphic over the entire inverted region. Finally, the appearance of segregating sites can be generated if duplicate...
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