SyMAP v3.4: a turnkey synteny system with application to plant genomes
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TLDR
SyMAP (Synteny Mapping and Analysis Program) was originally developed to compute synteny blocks between a sequenced genome and a FPC map, and has been extended to support pairs of sequenced genomes, illustrating their application to the study of genome duplication, differential gene loss and transitive homology between sorghum, maize and rice.Abstract:
SyMAP (Synteny Mapping and Analysis Program) was originally developed to compute synteny blocks between a sequenced genome and a FPC map, and has been extended to support pairs of sequenced genomes. SyMAP uses MUMmer to compute the raw hits between the two genomes, which are then clustered and filtered using the optional gene annotation. The filtered hits are input to the synteny algorithm, which was designed to discover duplicated regions and form larger-scale synteny blocks, where intervening micro-rearrangements are allowed. SyMAP provides extensive interactive Java displays at all levels of resolution along with simultaneous displays of multiple aligned pairs. The synteny blocks from multiple chromosomes may be displayed in a high-level dot plot or three-dimensional view, and the user may then drill down to see the details of a region, including the alignments of the hits to the gene annotation. These capabilities are illustrated by showing their application to the study of genome duplication, differential gene loss and transitive homology between sorghum, maize and rice. The software may be used from a website or standalone for the best performance. A project manager is provided to organize and automate the analysis of multi-genome groups. The software is freely distributed at http://www.agcol.arizona.edu/software/symap.read more
Citations
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MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity
Yupeng Wang,Haibao Tang,Jeremy D. DeBarry,Xu-fei Tan,Jingping Li,Xiyin Wang,Tae-Ho Lee,Huizhe Jin,Barry S. Marler,Hui Guo,Jessica C. Kissinger,Andrew H. Paterson +11 more
TL;DR: The MCScanX toolkit implements an adjusted MCScan algorithm for detection of synteny and collinearity that extends the original software by incorporating 14 utility programs for visualization of results and additional downstream analyses.
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OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy
David M. Emms,Steven L. Kelly +1 more
TL;DR: A novel orthogroups inference algorithm called OrthoFinder is provided that solves a previously undetected gene length bias in orthogroup inference, resulting in significant improvements in accuracy and utility.
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Draft genome sequence of chickpea ( Cicer arietinum ) provides a resource for trait improvement
Rajeev K. Varshney,Rajeev K. Varshney,Chi Song,Rachit K. Saxena,Sarwar Azam,Sheng Yu,Andrew G. Sharpe,Steven B. Cannon,Jong-Min Baek,Benjamin D. Rosen,Bunyamin Tar’an,Teresa Millán,Xudong Zhang,Larissa Ramsay,Aiko Iwata,Ying Wang,William Nelson,Andrew Farmer,Pooran M. Gaur,Carol Soderlund,R. Varma Penmetsa,Chunyan Xu,Arvind K. Bharti,Weiming He,Peter Winter,Shancen Zhao,James K. Hane,Noelia Carrasquilla-Garcia,Janet A. Condie,Hari D. Upadhyaya,Ming-Cheng Luo,Mahendar Thudi,C. L. L. Gowda,Narendra Singh,Judith Lichtenzveig,Krishna K. Gali,Josefa Rubio,N. Nadarajan,Jaroslav Dolezel,Kailash C. Bansal,Xun Xu,David Edwards,Gengyun Zhang,Guenter Kahl,Juan Gil,Karam B. Singh,Karam B. Singh,Swapan K. Datta,Scott A. Jackson,Jun Wang,Jun Wang,Douglas R. Cook +51 more
TL;DR: This work reports the ∼738-Mb draft whole genome shotgun sequence of CDC Frontier, a kabuli chickpea variety, which contains an estimated 28,269 genes, and identifies targets of both breeding-associated genetic sweeps and breeding- associated balancing selection.
Journal ArticleDOI
MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs
Jixian Zhai,Dong-Hoon Jeong,Emanuele De Paoli,Sunhee Park,Benjamin D. Rosen,Yupeng Li,Alvaro J. González,Zhe Yan,Sherry L. Kitto,Michael A. Grusak,Scott A. Jackson,Gary Stacey,Douglas R. Cook,Pamela J. Green,D. Janine Sherrier,Blake C. Meyers +15 more
TL;DR: The data reveal complex tasiRNA-based regulation of NB-LRRs that potentially evolved to facilitate symbiotic interactions and demonstrate miRNAs as master regulators of a large gene family via the targeting of highly conserved, protein-coding motifs, a new paradigm for miRNA function.
microRNAs as Master Regulators of the Plant NB-LRR Defense Gene Family via the Production of Phased, Trans-acting siRNAs
TL;DR: In this paper, a search for phased siRNAs (phasiRNAs) found at least 114 Medicago loci, the majority of which were defense-related NB-LRR-encoding genes.
References
More filters
Journal ArticleDOI
BLAT—The BLAST-Like Alignment Tool
TL;DR: How BLAT was optimized is described, which is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences.
Journal ArticleDOI
Circos: An information aesthetic for comparative genomics
Martin Krzywinski,Jacqueline E. Schein,Inanc Birol,Joseph M. Connors,Randy D. Gascoyne,Doug Horsman,Steven J.M. Jones,Marco A. Marra +7 more
TL;DR: Circos uses a circular ideogram layout to facilitate the display of relationships between pairs of positions by the use of ribbons, which encode the position, size, and orientation of related genomic elements.
Journal ArticleDOI
Versatile and open software for comparing large genomes
Stefan Kurtz,Adam M. Phillippy,Arthur L. Delcher,Michael E. Smoot,Martin Shumway,Corina Antonescu,Steven L. Salzberg +6 more
TL;DR: The newest version of MUMmer easily handles comparisons of large eukaryotic genomes at varying evolutionary distances, as demonstrated by applications to multiple genomes.
Journal ArticleDOI
The B73 Maize Genome: Complexity, Diversity, and Dynamics
Patrick S. Schnable,Doreen Ware,Robert S. Fulton,Joshua C. Stein,Fusheng Wei,Shiran Pasternak,Chengzhi Liang,Jianwei Zhang,Lucinda Fulton,Tina Graves,Patrick Minx,Amy Denise Reily,Laura Courtney,Scott Kruchowski,Chad Tomlinson,Cindy Strong,Kim D. Delehaunty,Catrina Fronick,Bill Courtney,Susan M. Rock,Eddie Belter,Feiyu Du,Kyung Kim,Rachel Abbott,Marc Cotton,Andrew Levy,Pamela Marchetto,Kerri Ochoa,Stephanie M. Jackson,Barbara Gillam,Weizu Chen,Le Yan,Jamey Higginbotham,Marco Cardenas,Jason Waligorski,Elizabeth Applebaum,Lindsey Phelps,Jason Falcone,Krishna L. Kanchi,T. K. Thane,Adam Scimone,Nay Thane,Jessica Henke,Thomas J. Wang,Jessica Ruppert,Neha Shah,Kelsi Rotter,Jennifer S. Hodges,Elizabeth Ingenthron,Matt Cordes,Sara Kohlberg,Jennifer Sgro,Brandon Delgado,Kelly Mead,Asif T. Chinwalla,Shawn Leonard,Kevin Crouse,Kristi Collura,Dave Kudrna,Jennifer Currie,Ruifeng He,Angelina Angelova,Shanmugam Rajasekar,Teri Mueller,Rene Lomeli,Gabriel Scara,Ara Ko,Krista Delaney,Marina Wissotski,Georgina Lopez,David Campos,Michele Braidotti,Elizabeth Ashley,Wolfgang Golser,Hyeran Kim,Seunghee Lee,Jinke Lin,Zeljko Dujmic,Woojin Kim,Jayson Talag,Andrea Zuccolo,Chuanzhu Fan,Aswathy Sebastian,Melissa Kramer,Lori Spiegel,Lidia Nascimento,Theresa Zutavern,Beth Miller,Claude Ambroise,Stephanie Muller,William Spooner,Apurva Narechania,Liya Ren,Sharon Wei,Sunita Kumari,Ben Faga,Michael J. Levy,Linda McMahan,Peter Van Buren,Matthew W. Vaughn,Kai Ying,Cheng Ting Yeh,Scott J. Emrich,Scott J. Emrich,Yi Jia,Ananth Kalyanaraman,Ananth Kalyanaraman,An-Ping Hsia,W. Brad Barbazuk,Regina S. Baucom,Thomas P. Brutnell,Nicholas C. Carpita,Cristian Chaparro,Jer Ming Chia,Jean-Marc Deragon,James C. Estill,Yan Fu,Jeffrey A. Jeddeloh,Yujun Han,Hye-Ran Lee,Pinghua Li,Damon Lisch,Sanzhen Liu,Zhijie Liu,Dawn H. Nagel,Maureen C. McCann,Phillip SanMiguel,Alan M. Myers,Dan Nettleton,John D. Nguyen,Bryan W. Penning,Lalit Ponnala,Kevin L. Schneider,David C. Schwartz,Anupma Sharma,Carol Soderlund,Nathan M. Springer,Qi Sun,Hao Wang,Michael S. Waterman,Richard P. Westerman,Thomas K. Wolfgruber,Lixing Yang,Yeisoo Yu,Lifang Zhang,Shiguo Zhou,Qihui Zhu,Jeffrey L. Bennetzen,R. Kelly Dawe,Jiming Jiang,Ning Jiang,Gernot G. Presting,Susan R. Wessler,Srinivas Aluru,Srinivas Aluru,Robert A. Martienssen,Sandra W. Clifton,W. Richard McCombie,Rod A. Wing,Richard K. Wilson +159 more
TL;DR: The sequence of the maize genome reveals it to be the most complex genome known to date and the correlation of methylation-poor regions with Mu transposon insertions and recombination and how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state is reported.
Journal ArticleDOI
Mauve: multiple alignment of conserved genomic sequence with rearrangements.
TL;DR: This work presents methods for identification and alignment of conserved genomic DNA in the presence of rearrangements and horizontal transfer and evaluated the quality of Mauve alignments and drawn comparison to other methods through extensive simulations of genome evolution.