Informatics Publications

• 2011
• 2010
• 2009
• 2008

Plant genome assembly, annotation and analysis methods are presented in the scientific publications listed below, as follows:

• Ref 1 describes the development of a new algorithm for short-read assembly of small and large genomes, and benchmarks it against other available assemblers on a fungal dataset from Illumina as well as an E. coli dataset commonly used as a benchmark.
• Refs 2, 4, 5, 7, 8, 11, 14, and 17 describe the development and subsequent improvements of a pipeline for annotating protein-coding genes in complex repetitive genomes in plants and animals, including the identification and masking of repeats, use of homology and ab initio methods for gene prediction, and integration of EST and cDNA datasets. This pipeline is used group for the annotation of plant genomes.
• Refs 2, 4, 5, 7, 8, 11, 16, 17, describes novel methods for computing and analyzing conserved colinearity and general synteny (conserved linkage) among genomes. These methods led to the identification of ancient conserved linkage groups in animals and conserved chromosomal colinearity in plants. Various analyses of the nature of conserved duplicated genes, conserved intron position and phase, etc. are also included.
• Refs 2-8, 11, 14, 16, 17, 18, 21, describe methods for the analysis of orthology and paralogy using diverse inputs including synonymous transversions, synteny, domain content, and phylogenetic considerations. Different genome analyses use different inputs as appropriate based on phylogenetic position. These methods have led to the analysis of gene families characteristic of plants and animals, including the identification of core "ancestral" gene sets for these clades.

2011

1. Meraculous: de novo genome assembly with short paired-end reads. Chapman JA, Ho I, Sunkara S, Luo S, Schroth GP, Rokhsar DS. PLOS One submitted

2010

1. The Amphimedon queenslandica genome and the evolution of animal complexity. Srivastava M, Simakov O, Chapman J, Fahey B, Gauthier ME, Mitros T, Richards GS, Conaco C, Dacre M, Hellsten U, Larroux C, Putnam NH, Stanke M, Adamska M, Darling A, Degnan SM, Oakley TH, Plachetzki DC, Zhai Y, Adamski M, Calcino A, Cummins SF, Goodstein DM, Harris C, Jackson DJ, Leys SP, Shu S, Woodcroft BJ, Vervoort M, Kosik KS, Manning G, Degnan BM, Rokhsar DS. Nature. 2010 Aug 5;466(7307):720-6.PMID: 20686567
2. Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri. Prochnik SE, Umen J, Nedelcu AM, Hallmann A, Miller SM, Nishii I, Ferris P, Kuo A, Mitros T, Fritz-Laylin LK, Hellsten U, Chapman J, Simakov O, Rensing SA, Terry A, Pangilinan J, Kapitonov V, Jurka J, Salamov A, Shapiro H, Schmutz J, Grimwood J, Lindquist E, Lucas S, Grigoriev IV, Schmitt R, Kirk D, Rokhsar DS. Science . 2010 Jul 9;329(5988):223-6.PMID:
3. The genome of the Western clawed frog Xenopus tropicalis. Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu S, Taher L, Blitz IL, Blumberg B, Dichmann DS, Dubchak I, Amaya E, Detter JC, Fletcher R, Gerhard DS, Goodstein D, Graves T, Grigoriev IV, Grimwood J, Kawashima T, Lindquist E, Lucas SM, Mead PE, Mitros T, Ogino H, Ohta Y, Poliakov AV, Pollet N, Robert J, Salamov A, Sater AK, Schmutz J, Terry A, Vize PD, Warren WC, Wells D, Wills A, Wilson RK, Zimmerman LB, Zorn AM, Grainger R, Grammer T, Khokha MK, Richardson PM, Rokhsar DS. Science . 2010 Apr 30;328(5978):633-6. PMID: 20431018
4. The dynamic genome of Hydra. Chapman JA, Kirkness EF, Simakov O, Hampson SE, Mitros T, Weinmaier T, Rattei T, Balasubramanian PG, Borman J, Busam D, Disbennett K, Pfannkoch C, Sumin N, Sutton GG, Viswanathan LD, Walenz B, Goodstein DM, Hellsten U, Kawashima T, Prochnik SE, Putnam NH, Shu S, Blumberg B, Dana CE, Gee L, Kibler DF, Law L, Lindgens D, Martinez DE, Peng J, Wigge PA, Bertulat B, Guder C, Nakamura Y, Ozbek S, Watanabe H, Khalturin K, Hemmrich G, Franke A, Augustin R, Fraune S, Hayakawa E, Hayakawa S, Hirose M, Hwang JS, Ikeo K, Nishimiya-Fujisawa C, Ogura A, Takahashi T, Steinmetz PR, Zhang X, Aufschnaiter R, Eder MK, Gorny AK, Salvenmoser W, Heimberg AM, Wheeler BM, Peterson KJ, Böttger A, Tischler P, Wolf A, Gojobori T, Remington KA, Strausberg RL, Venter JC, Technau U, Hobmayer B, Bosch TC, Holstein TW, Fujisawa T, Bode HR, David CN, Rokhsar DS, Steele RE. Nature. 2010 Mar 25;464(7288):592-6. PMID: 20228792
5. The genome of Naegleria gruberi illuminates early eukaryotic versatility. Fritz-Laylin LK, Prochnik SE, Ginger ML, Dacks JB, Carpenter ML, Field MC, Kuo A, Paredez A, Chapman J, Pham J, Shu S, Neupane R, Cipriano M, Mancuso J, Tu H, Salamov A, Lindquist E, Shapiro H, Lucas S, Grigoriev IV, Cande WZ, Fulton C, Rokhsar DS, Dawson SC. Cell. 2010 Mar 5;140(5):631-42. PMID: 20211133
6. Genome sequencing and analysis of the model grass Brachypodium distachyon. International Brachypodium Initiative. Nature. 2010 Feb 11;463(7282):763-8.PMID: 20148030
7. Genome sequence of the palaeopolyploid soybean. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang XC, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA. Nature. 2010 Jan 14;463(7278):178-83. Erratum in: Nature. 2010 May 6;465(7294):120. PMID: 20075913

2009

1. Domain shuffling and the evolution of vertebrates. Kawashima T, Kawashima S, Tanaka C, Murai M, Yoneda M, Putnam NH, Rokhsar DS, Kanehisa M, Satoh N, Wada H. Genome Res. 2009 Aug;19(8):1393-403. Epub 2009 May 14.PMID: 19443856
2. Old can be new again: HAPPY whole genome sequencing, mapping and assembly. Jiang Z, Rokhsar DS, Harland RM. Int J Biol Sci. 2009;5(4):298-303. Erratum: Int J Biol Sci. 2009;5(6):621. PMID: 19381348
3. The Sorghum bicolor genome and the diversification of grasses. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboob-ur-Rahman, Ware D, Westhoff P, Mayer KF, Messing J, Rokhsar DS. Nature.. 2009 Jan 29;457(7229):551-6.PMID: 19189423

2008

1. The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome.12. Sela DA, Chapman J, Adeuya A, Kim JH, Chen F, Whitehead TR, Lapidus A, Rokhsar DS, Lebrilla CB, German JB, Price NP, Richardson PM, Mills DA. Proc Natl Acad Sci U S A. 2008 Dec 2;105(48):18964-9. PMID: 19033196
2. Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Grimson A, Srivastava M, Fahey B, Woodcroft BJ, Chiang HR, King N, Degnan BM, Rokhsar DS, Bartel DP. Nature. 2008 Oct 30;455(7217):1193-7. PMID: 18830242
3. Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism. Opperman CH, Bird DM, Williamson VM, Rokhsar DS, Burke M, Cohn J, Cromer J, Diener S, Gajan J, Graham S, Houfek TD, Liu Q, Mitros T, Schaff J, Schaffer R, Scholl E, Sosinski BR, Thomas VP, Windham E. Proc Natl Acad Sci U S A. 2008 Sep 30;105(39):14802-7. PMID: 18809916
4. Rapid whole-genome mutational profiling using next-generation sequencing technologies. Smith DR, Quinlan AR, Peckham HE, Makowsky K, Tao W, Woolf B, Shen L, Donahue WF, Tusneem N, Stromberg MP, Stewart DA, Zhang L, Ranade SS, Warner JB, Lee CC, Coleman BE, Zhang Z, McLaughlin SF, Malek JA, Sorenson JM, Blanchard AP, Chapman J, Hillman D, Chen F, Rokhsar DS, McKernan KJ, Jeffries TW, Marth GT, Richardson PM. Genome Res. 2008 Oct;18(10):1638-42. PMID: 18775913
5. The Trichoplax genome and the nature of placozoans. Srivastava M, Begovic E, Chapman J, Putnam NH, Hellsten U, Kawashima T, Kuo A, Mitros T, Salamov A, Carpenter ML, Signorovitch AY, Moreno MA, Kamm K, Grimwood J, Schmutz J, Shapiro H, Grigoriev IV, Buss LW, Schierwater B, Dellaporta SL, Rokhsar DS. Nature. 2008 Aug 21;454(7207):955-60.PMID: 18719581
6. The amphioxus genome and the evolution of the chordate karyotype. Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK, Benito-Gutiérrez EL, Dubchak I, Garcia-Fernàndez J, Gibson-Brown JJ, Grigoriev IV, Horton AC, de Jong PJ, Jurka J, Kapitonov VV, Kohara Y, Kuroki Y, Lindquist E, Lucas S, Osoegawa K, Pennacchio LA, Salamov AA, Satou Y, Sauka-Spengler T, Schmutz J, Shin-I T, Toyoda A, Bronner-Fraser M, Fujiyama A, Holland LZ, Holland PW, Satoh N, Rokhsar DS. Nature. 2008 Jun 19;453(7198):1064-71.PMID: 18563158
7. The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Holland LZ, Albalat R, Azumi K, Benito-Gutiérrez E, Blow MJ, Bronner-Fraser M, Brunet F, Butts T, Candiani S, Dishaw LJ, Ferrier DE, Garcia-Fernàndez J, Gibson-Brown JJ, Gissi C, Godzik A, Hallböök F, Hirose D, Hosomichi K, Ikuta T, Inoko H, Kasahara M, Kasamatsu J, Kawashima T, Kimura A, Kobayashi M, Kozmik Z, Kubokawa K, Laudet V, Litman GW, McHardy AC, Meulemans D, Nonaka M, Olinski RP, Pancer Z, Pennacchio LA, Pestarino M, Rast JP, Rigoutsos I, Robinson-Rechavi M, Roch G, Saiga H, Sasakura Y, Satake M, Satou Y, Schubert M, Sherwood N, Shiina T, Takatori N, Tello J, Vopalensky P, Wada S, Xu A, Ye Y, Yoshida K, Yoshizaki F, Yu JK, Zhang Q, Zmasek CM, de Jong PJ, Osoegawa K, Putnam NH, Rokhsar DS, Satoh N, Holland PW. Genome Res. 2008 Jul;18(7):1100-11. Erratum: Genome Res. 2008 Aug;18(8):1380. PMID: 18562680
8. Promoter elements associated with RNA Pol II stalling in the Drosophila embryo. Hendrix DA, Hong JW, Zeitlinger J, Rokhsar DS, Levine MS. Proc Natl Acad Sci U S A. 2008 Jun 3;105(22):7762-7. PMID: 18505835
9. Genesis and expansion of metazoan transcription factor gene classes. Larroux C, Luke GN, Koopman P, Rokhsar DS, Shimeld SM, Degnan BM. Mol Biol Evol. 2008 May;25(5):980-96. PMID: 18296413
10. The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans.. King N, Westbrook MJ, Young SL, Kuo A, Abedin M, Chapman J, Fairclough S, Hellsten U, Isogai Y, Letunic I, Marr M, Pincus D, Putnam N, Rokas A, Wright KJ, Zuzow R, Dirks W, Good M, Goodstein D, Lemons D, Li W, Lyons JB, Morris A, Nichols S, Richter DJ, Salamov A, JGI Sequencing, Bork P, Lim WA, Manning G, Miller WT, McGinnis W, Shapiro H, Tjian R, Grigoriev IV, Rokhsar D. Nature. 2008 Feb 14;451(7180):783-8. PMID: 18273011