Searching journal content for articles similar to Song et al. 12 (10): 1549.

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  1. Research: Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize
    • Baoxing Song,
    • Edward S. Buckler,
    • Hai Wang,
    • Yaoyao Wu,
    • Evan Rees,
    • Elizabeth A. Kellogg,
    • Daniel J. Gates,
    • Merritt Khaipho-Burch,
    • Peter J. Bradbury,
    • Jeffrey Ross-Ibarra,
    • Matthew B. Hufford,
    • and M. Cinta Romay
    Genome Res. July 2021 31: 1245-1257; Published in Advance May 27, 2021, doi:10.1101/gr.266528.120
    ...; Rodgers-Melnick et al. 2016; Oka et al. 2017; Wang et al. 2017b; Li et al. 2019; Lu et al. 2019; Ricci et al. 2019; Tu et al. 2020) with CNSs could provide new insight into understudied noncoding fractions of the .Genomes of the grass tribe Andropogoneae provide a valuable and powerful system...
  2. Research: Gene duplication and genetic innovation in cereal genomes
    • Hui Guo,
    • Yuannian Jiao,
    • Xu Tan,
    • Xiyin Wang,
    • Xianzhong Huang,
    • Huizhe Jin,
    • and Andrew H. Paterson
    Genome Res. February 2019 29: 261-269; Published in Advance January 16, 2019, doi:10.1101/gr.237511.118
    ..., Carica (papaya), and Theobroma (cacao) experienced hexaploidization ∼110 million years ago (mya) with no further WGD thereafter (Jaillon et al. 2007). Three ancient WGDs shaped the ancestral lineage of grasses (Jiao et al. 2014); however, Oryza sativa (rice) and Sorghum bicolor (sorghum) experienced...
  3. Research: Drought responsive gene expression regulatory divergence between upland and lowland ecotypes of a perennial C4 grass
    • John T. Lovell,
    • Scott Schwartz,
    • David B. Lowry,
    • Eugene V. Shakirov,
    • Jason E. Bonnette,
    • Xiaoyu Weng,
    • Mei Wang,
    • Jenifer Johnson,
    • Avinash Sreedasyam,
    • Christopher Plott,
    • Jerry Jenkins,
    • Jeremy Schmutz,
    • and Thomas E. Juenger
    Genome Res. April 2016 26: 510-518; Published in Advance March 7, 2016, doi:10.1101/gr.198135.115
    ...grass Genome Research 515 www..org sequencer using a TruSeq SBS sequencing kit (200 cycles, v3, following a 2 × 150 indexed run recipe). Raw readswere trimmed, thenmapped to the draft v1.1 P. hallii var. filipes (which is from the FIL2 accession), and counts were called for each of the 37,638 annotated...
  4. Resource: Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions
    • Rodrigo P. Baptista,
    • Yiran Li,
    • Adam Sateriale,
    • Mandy J. Sanders,
    • Karen L. Brooks,
    • Alan Tracey,
    • Brendan R.E. Ansell,
    • Aaron R. Jex,
    • Garrett W. Cooper,
    • Ethan D. Smith,
    • Rui Xiao,
    • Jennifer E. Dumaine,
    • Peter Georgeson,
    • Bernard J. Pope,
    • Matthew Berriman,
    • Boris Striepen,
    • James A. Cotton,
    • and Jessica C. Kissinger
    Genome Res. January 2022 32: 203-213; Published in Advance November 11, 2021, doi:10.1101/gr.275325.121
    ...of Arizona, Sterling Parasitology Laboratory. It is a GP60 subtype (IIa) like the current C. parvum IOWA II reference (CpIRef) sequence. C. parvum IOWA DNA was also prepared from oocysts obtained in 2018 from Bunch Grass Farms, Deary, Idaho, referred to as CpBGF in this study. C. parvum KSU-1 genomic DNA...
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  5. Method: In silico phylogenomics using complete genomes: a case study on the evolution of hominoids
    • Igor Rodrigues Costa,
    • Francisco Prosdocimi,
    • and W. Bryan Jennings
    Genome Res. September 2016 26: 1257-1267; Published in Advance July 19, 2016, doi:10.1101/gr.203950.115
    ...@gmail.com ↵ 3 These authors contributed equally to this work. Abstract The increasing availability of complete genome data is facilitating the acquisition of phylogenomic data sets, but the process of obtaining orthologous sequences from other genomes and assembling multiple sequence alignments...
  6. Research: Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution
    • Florent Murat,
    • Jian-Hong Xu,
    • Eric Tannier,
    • Michael Abrouk,
    • Nicolas Guilhot,
    • Caroline Pont,
    • Joachim Messing,
    • and Jérôme Salse
    Genome Res. November 2010 20: 1545-1557; Published in Advance September 28, 2010, doi:10.1101/gr.109744.110
    ..., where a number of genomes have now been sequenced. Based on detailed paleogenomics, using inference from n = 5–12 grass ancestral karyotypes (AGKs) in terms of gene content and order, we delineated sequence intervals comprising a complete set of junction break points of orthologous regions from rice...
  7. Research: Localized hypermutation and associated gene losses in legume chloroplast genomes
    • Alan M. Magee,
    • Sue Aspinall,
    • Danny W. Rice,
    • Brian P. Cusack,
    • Marie Sémon,
    • Antoinette S. Perry,
    • Saša Stefanović,
    • Dan Milbourne,
    • Susanne Barth,
    • Jeffrey D. Palmer,
    • John C. Gray,
    • Tony A. Kavanagh,
    • and Kenneth H. Wolfe
    Genome Res. December 2010 20: 1700-1710; Published in Advance October 26, 2010, doi:10.1101/gr.111955.110
    .... 2005). The loss in Trifolium is one of five separate known instances of loss of accD in angiosperm cpDNAs (Supplemental Table S1). In grass species—the only case that has been studied in detail—the prokaryoticmultisubunit carboxylase in the plastid has been completely replaced by a nuclear...
  8. Research: Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes
    • Konstantinos Kritsas,
    • Samuel E. Wuest,
    • Daniel Hupalo,
    • Andrew D. Kern,
    • Thomas Wicker,
    • and Ueli Grossniklaus
    Genome Res. December 2012 22: 2455-2466; Published in Advance September 17, 2012, doi:10.1101/gr.129346.111
    ...have been proposed to play important roles in gene regulation, RNA processing, and maintaining genome integrity. However, because all of these functions can tolerate some sequence variation, their ultraconserved and ultraselected nature is not explained. We investigated whether there are highly...
    OPEN ACCESS ARTICLE
  9. LETTER: Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species Genome Res. September 2005 15: 1284-1291; Published in Advance August 18, 2005, doi:10.1101/gr.3869505
    ...Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species The Rice Chromosome 3 Sequencing Consortium 1 , 2 Abstract Rice ( Oryza sativa L.) chromosome 3 is evolutionarily conserved across the cultivated cereals and shares large...
  10. Research: Patching gaps in plant genomes results in gene movement and erosion of colinearity
    • Thomas Wicker,
    • Jan P. Buchmann,
    • and Beat Keller
    Genome Res. September 2010 20: 1229-1237; Published in Advance June 7, 2010, doi:10.1101/gr.107284.110
    .... Trends Plant Sci 4: 263–269. Hartlerode AJ, Scully R. 2009. Mechanisms of double-strand break repair in somatic mammalian cells. Biochem J 423: 157–168. International Brachypodium Initiative. 2010. Genome sequencing and analysis of themodel grassBrachypodiumdistachyon.Nature463:763–768. International...
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