Hollmer M (2013) Roche to close 454 life sciences as it reduces gene sequencing focus.
FierceBiotech:
https://www.fiercebiotech.com/medical-devices/roche-to-close-454-life-sci
ences-as-it-reduces-gene-sequencing-focus
Holt C, Yandell M (2011) MAKER2: an annotation pipeline and genome-database management
tool for second-generation genome projects. BMC Bioinformatics 12:491
Hori K, Maruyama F, Fujisawa T, Togashi T, Yamamoto N, Seo M, Sato S, Yamada T, Mori H,
Tajima N, Moriyama T, Ikeuchi M, Watanabe M, Wada H, Kobayashi K, Saito M, Masuda T,
Sasaki-Sekimoto Y, Mashiguchi K, Awai K, Shimojima M, Masuda S, Iwai M, Nobusawa T,
Narise T, Kondo S, Saito H, Sato R, Murakawa M, Ihara Y, Oshima-Yamada Y, Ohtaka K,
Satoh M, Sonobe K, Ishii M, Ohtani R, Kanamori-Sato M, Honoki R, Miyazaki D,
Mochizuki H, Umetsu J, Higashi K, Shibata D, Kamiya Y, Sato N, Nakamura Y, Tabata S,
Ida S, Kurokawa K, Ohta H (2014) Klebsormidium flaccidum genome reveals primary factors
for plant terrestrial adaptation. Nat Commun 5:3978
Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9(9):868–877
Hutcheon C, Ditt RF, Beilstein M, Comai L, Schroeder J, Goldstein E, Shewmaker CK, Nguyen T,
De Rocher J, Kiser J (2010) Polyploid genome of Camelina sativa revealed by isolation of fatty
acid synthesis genes. BMC Plant Biol 10:233
Ibarra-Laclette E, Lyons E, Hernandez-Guzman G, Perez-Torres CA, Carretero-Paulet L, Chang
TH, Lan T, Welch AJ, Juarez MJ, Simpson J, Fernandez-Cortes A, Arteaga-Vazquez M,
Gongora-Castillo E, Acevedo-Hernandez G, Schuster SC, Himmelbauer H, Minoche AE,
Xu S, Lynch M, Oropeza-Aburto A, Cervantes-Perez SA, de Jesus Ortega-Estrada M,
Cervantes-Luevano JI, Michael TP, Mockler T, Bryant D, Herrera-Estrella A, Albert VA,
Herrera-Estrella L (2013) Architecture and evolution of a minute plant genome. Nature
498(7452):94–98
International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass
Brachypodium distachyon. Nature 463(7282):763–768
International Peach Genome Initiative, Verde I, Abbott AG, Scalabrin S, Jung S, Shu S, Marroni F,
Zhebentyayeva T, Dettori MT, Grimwood J, Cattonaro F, Zuccolo A, Rossini L, Jenkins J,
Vendramin E, Meisel LA, Decroocq V, Sosinski B, Prochnik S, Mitros T, Policriti A,
Cipriani G, Dondini L, Ficklin S, Goodstein DM, Xuan P, Del Fabbro C, Aramini V,
Copetti D, Gonzalez S, Horner DS, Falchi R, Lucas S, Mica E, Maldonado J, Lazzari B,
Bielenberg D, Pirona R, Miculan M, Barakat A, Testolin R, Stella A, Tartarini S, Tonutti P,
Arus P, Orellana A, Wells C, Main D, Vizzotto G, Silva H, Salamini F, Schmutz J, Morgante M,
Rokhsar DS (2013) The high-quality draft genome of peach (Prunus persica) identifies unique
patterns of genetic diversity, domestication and genome evolution. Nat Genet 45(5):487–494
International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome.
Nature 436(7052):793–800
Isono K, McIninch JD, Borodovsky M (1994) Characteristic features of the nucleotide sequences of
yeast mitochondrial ribosomal protein genes as analyzed by computer program GeneMark.
DNA Res 1(6):263–269
Ištvánek J, Jaroš M, Krenek A, Řepková J (2014) Genome assembly and annotation for red clover
(Trifolium pratense; Fabaceae). Am J Bot 101(2):327–337
Iyer BV, Kenward M, Arya G (2011) Hierarchies in eukaryotic genome organization: insights from
polymer theory and simulations. BMC Biophys 4:8
Jackman SD, Vandervalk BP, Mohamadi H, Chu J, Yeo S, Hammond SA, Jahesh G, Khan H,
Coombe L, Warren RL, Birol I (2017) ABySS 2.0: resource-efficient assembly of large genomes
using a Bloom filter. Genome Res 27(5):768–777
Jackson SA (2016) Rice: the first crop genome. Rice 9(1):14
Jaffe JD, Berg HC, Church GM (2004) Proteogenomic mapping as a complementary method to
perform genome annotation. Proteomics 4(1):59–77
Jain M, Olsen HE, Paten B, Akeson M (2016) The Oxford nanopore MinION: delivery of nanopore
sequencing to the genomics community. Genome Biol 17(1):239
Sequencing Plant Genomes
181
FierceBiotech:
https://www.fiercebiotech.com/medical-devices/roche-to-close-454-life-sci
ences-as-it-reduces-gene-sequencing-focus
Holt C, Yandell M (2011) MAKER2: an annotation pipeline and genome-database management
tool for second-generation genome projects. BMC Bioinformatics 12:491
Hori K, Maruyama F, Fujisawa T, Togashi T, Yamamoto N, Seo M, Sato S, Yamada T, Mori H,
Tajima N, Moriyama T, Ikeuchi M, Watanabe M, Wada H, Kobayashi K, Saito M, Masuda T,
Sasaki-Sekimoto Y, Mashiguchi K, Awai K, Shimojima M, Masuda S, Iwai M, Nobusawa T,
Narise T, Kondo S, Saito H, Sato R, Murakawa M, Ihara Y, Oshima-Yamada Y, Ohtaka K,
Satoh M, Sonobe K, Ishii M, Ohtani R, Kanamori-Sato M, Honoki R, Miyazaki D,
Mochizuki H, Umetsu J, Higashi K, Shibata D, Kamiya Y, Sato N, Nakamura Y, Tabata S,
Ida S, Kurokawa K, Ohta H (2014) Klebsormidium flaccidum genome reveals primary factors
for plant terrestrial adaptation. Nat Commun 5:3978
Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9(9):868–877
Hutcheon C, Ditt RF, Beilstein M, Comai L, Schroeder J, Goldstein E, Shewmaker CK, Nguyen T,
De Rocher J, Kiser J (2010) Polyploid genome of Camelina sativa revealed by isolation of fatty
acid synthesis genes. BMC Plant Biol 10:233
Ibarra-Laclette E, Lyons E, Hernandez-Guzman G, Perez-Torres CA, Carretero-Paulet L, Chang
TH, Lan T, Welch AJ, Juarez MJ, Simpson J, Fernandez-Cortes A, Arteaga-Vazquez M,
Gongora-Castillo E, Acevedo-Hernandez G, Schuster SC, Himmelbauer H, Minoche AE,
Xu S, Lynch M, Oropeza-Aburto A, Cervantes-Perez SA, de Jesus Ortega-Estrada M,
Cervantes-Luevano JI, Michael TP, Mockler T, Bryant D, Herrera-Estrella A, Albert VA,
Herrera-Estrella L (2013) Architecture and evolution of a minute plant genome. Nature
498(7452):94–98
International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass
Brachypodium distachyon. Nature 463(7282):763–768
International Peach Genome Initiative, Verde I, Abbott AG, Scalabrin S, Jung S, Shu S, Marroni F,
Zhebentyayeva T, Dettori MT, Grimwood J, Cattonaro F, Zuccolo A, Rossini L, Jenkins J,
Vendramin E, Meisel LA, Decroocq V, Sosinski B, Prochnik S, Mitros T, Policriti A,
Cipriani G, Dondini L, Ficklin S, Goodstein DM, Xuan P, Del Fabbro C, Aramini V,
Copetti D, Gonzalez S, Horner DS, Falchi R, Lucas S, Mica E, Maldonado J, Lazzari B,
Bielenberg D, Pirona R, Miculan M, Barakat A, Testolin R, Stella A, Tartarini S, Tonutti P,
Arus P, Orellana A, Wells C, Main D, Vizzotto G, Silva H, Salamini F, Schmutz J, Morgante M,
Rokhsar DS (2013) The high-quality draft genome of peach (Prunus persica) identifies unique
patterns of genetic diversity, domestication and genome evolution. Nat Genet 45(5):487–494
International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome.
Nature 436(7052):793–800
Isono K, McIninch JD, Borodovsky M (1994) Characteristic features of the nucleotide sequences of
yeast mitochondrial ribosomal protein genes as analyzed by computer program GeneMark.
DNA Res 1(6):263–269
Ištvánek J, Jaroš M, Krenek A, Řepková J (2014) Genome assembly and annotation for red clover
(Trifolium pratense; Fabaceae). Am J Bot 101(2):327–337
Iyer BV, Kenward M, Arya G (2011) Hierarchies in eukaryotic genome organization: insights from
polymer theory and simulations. BMC Biophys 4:8
Jackman SD, Vandervalk BP, Mohamadi H, Chu J, Yeo S, Hammond SA, Jahesh G, Khan H,
Coombe L, Warren RL, Birol I (2017) ABySS 2.0: resource-efficient assembly of large genomes
using a Bloom filter. Genome Res 27(5):768–777
Jackson SA (2016) Rice: the first crop genome. Rice 9(1):14
Jaffe JD, Berg HC, Church GM (2004) Proteogenomic mapping as a complementary method to
perform genome annotation. Proteomics 4(1):59–77
Jain M, Olsen HE, Paten B, Akeson M (2016) The Oxford nanopore MinION: delivery of nanopore
sequencing to the genomics community. Genome Biol 17(1):239
Sequencing Plant Genomes
181