Cavalier-Smith T (2005) Economy, speed and size matter: evolutionary forces driving nuclear
genome miniaturization and expansion. Ann Bot 95(1):147–175
Chagné D (2015) Whole genome sequencing of fruit tree species. Adv Bot Res 74:1–37
Chapman AD (2009) Numbers of living species in Australia and the World, 2nd edn. Australian
Government Department of the Environment, Water, Heritage and the Arts, Canberra
Charlesworth B (2006) The evolutionary biology of sex. Curr Biol 16(17):R693–R695
Chen J, Huang Q, Gao D, Wang J, Lang Y, Liu T, Li B, Bai Z, Luis Goicoechea J, Liang C, Chen C,
Zhang W, Sun S, Liao Y, Zhang X, Yang L, Song C, Wang M, Shi J, Liu G, Liu J, Zhou H,
Zhou W, Yu Q, An N, Chen Y, Cai Q, Wang B, Liu B, Min J, Huang Y, Wu H, Li Z, Zhang Y,
Yin Y, Song W, Jiang J, Jackson SA, Wing RA, Wang J, Chen M (2013a) Whole-genome
sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. Nat
Commun 4:1595
Chen M, Zhao Z, Chen L, Zhou F, Zhong Z, Jiang L, Wan J (2013b) Genetic analysis and fine
mapping of a semi-dwarf gene in a centromeric region in rice (Oryza sativa L.) Breed Sci
63(2):164–168
Claros MG, Bautista R, Guerrero-Fernandez D, Benzerki H, Seoane P, Fernandez-Pozo N (2012)
Why assembling plant genome sequences is so challenging. Biology 1(2):439–459
Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F,
Wilczynski B, de Hoon MJ (2009) Biopython: freely available Python tools for computational
molecular biology and bioinformatics. Bioinformatics 25(11):1422–1423
Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szczesniak MW,
Gaffney DJ, Elo LL, Zhang X, Mortazavi A (2016) A survey of best practices for RNA-seq data
analysis. Genome Biol 17:13
Copetti D, Zhang J, El Baidouri M, Gao D, Wang J, Barghini E, Cossu RM, Angelova A,
Maldonado LC, Roffler S, Ohyanagi H, Wicker T, Fan C, Zuccolo A, Chen M, Costa de
Oliveira A, Han B, Henry R, Hsing YI, Kurata N, Wang W, Jackson SA, Panaud O, Wing RA
(2015) RiTE database: a resource database for genus-wide rice genomics and evolutionary
biology. BMC Genomics 16:538
Corradi N, Pombert JF, Farinelli L, Didier ES, Keeling PJ (2010) The complete sequence of the
smallest known nuclear genome from the microsporidian Encephalitozoon intestinalis.
Nat Commun 1:77
D’Hont A, Denoeud F, Aury JM, Baurens FC, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G,
Rouard M, Da Silva C, Jabbari K, Cardi C, Poulain J, Souquet M, Labadie K, Jourda C,
Lengelle J, Rodier-Goud M, Alberti A, Bernard M, Correa M, Ayyampalayam S, McKain MR,
Leebens-Mack J, Burgess D, Freeling M, Mbeguie AMD, Chabannes M, Wicker T, Panaud O,
Barbosa J, Hribova E, Heslop-Harrison P, Habas R, Rivallan R, Francois P, Poiron C, Kilian A,
Burthia D, Jenny C, Bakry F, Brown S, Guignon V, Kema G, Dita M, Waalwijk C, Joseph S,
Dievart A, Jaillon O, Leclercq J, Argout X, Lyons E, Almeida A, Jeridi M, Dolezel J, Roux N,
Risterucci AM, Weissenbach J, Ruiz M, Glaszmann JC, Quetier F, Yahiaoui N, Wincker P
(2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants.
Nature 488(7410):213–217
Dar T-U-H, Ruhman R-U (2017) Occurrence of polyploidy. In: Polyploidy: recent trends and future
perspectives. Springer, New Dehli, pp 31–42
Dassanayake M, Oh DH, Haas JS, Hernandez A, Hong H, Ali S, Yun DJ, Bressan RA, Zhu JK,
Bohnert HJ, Cheeseman JM (2011) The genome of the extremophile crucifer Thellungiella
parvula. Nat Genet 43(9):913–918
de Vries J, Archibald JM (2018) Plant evolution: landmarks on the path to terrestrial life.
New Phytol 217(4):1428–1434
Denker A, De Laat W (2016) The second decade of 3C technologies: detailed insights into nuclear
organization. Genes Dev 30(12):1357–1382
Derelle E, Ferraz C, Rombauts S, Rouze P, Worden AZ, Robbens S, Partensky F, Degroeve S,
Echeynie S, Cooke R, Saeys Y, Wuyts J, Jabbari K, Bowler C, Panaud O, Piegu B, Ball SG, Ral
JP, Bouget FY, Piganeau G, De Baets B, Picard A, Delseny M, Demaille J, Van de Peer Y,
178
D. G. Peterson and M. Arick
genome miniaturization and expansion. Ann Bot 95(1):147–175
Chagné D (2015) Whole genome sequencing of fruit tree species. Adv Bot Res 74:1–37
Chapman AD (2009) Numbers of living species in Australia and the World, 2nd edn. Australian
Government Department of the Environment, Water, Heritage and the Arts, Canberra
Charlesworth B (2006) The evolutionary biology of sex. Curr Biol 16(17):R693–R695
Chen J, Huang Q, Gao D, Wang J, Lang Y, Liu T, Li B, Bai Z, Luis Goicoechea J, Liang C, Chen C,
Zhang W, Sun S, Liao Y, Zhang X, Yang L, Song C, Wang M, Shi J, Liu G, Liu J, Zhou H,
Zhou W, Yu Q, An N, Chen Y, Cai Q, Wang B, Liu B, Min J, Huang Y, Wu H, Li Z, Zhang Y,
Yin Y, Song W, Jiang J, Jackson SA, Wing RA, Wang J, Chen M (2013a) Whole-genome
sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. Nat
Commun 4:1595
Chen M, Zhao Z, Chen L, Zhou F, Zhong Z, Jiang L, Wan J (2013b) Genetic analysis and fine
mapping of a semi-dwarf gene in a centromeric region in rice (Oryza sativa L.) Breed Sci
63(2):164–168
Claros MG, Bautista R, Guerrero-Fernandez D, Benzerki H, Seoane P, Fernandez-Pozo N (2012)
Why assembling plant genome sequences is so challenging. Biology 1(2):439–459
Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F,
Wilczynski B, de Hoon MJ (2009) Biopython: freely available Python tools for computational
molecular biology and bioinformatics. Bioinformatics 25(11):1422–1423
Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szczesniak MW,
Gaffney DJ, Elo LL, Zhang X, Mortazavi A (2016) A survey of best practices for RNA-seq data
analysis. Genome Biol 17:13
Copetti D, Zhang J, El Baidouri M, Gao D, Wang J, Barghini E, Cossu RM, Angelova A,
Maldonado LC, Roffler S, Ohyanagi H, Wicker T, Fan C, Zuccolo A, Chen M, Costa de
Oliveira A, Han B, Henry R, Hsing YI, Kurata N, Wang W, Jackson SA, Panaud O, Wing RA
(2015) RiTE database: a resource database for genus-wide rice genomics and evolutionary
biology. BMC Genomics 16:538
Corradi N, Pombert JF, Farinelli L, Didier ES, Keeling PJ (2010) The complete sequence of the
smallest known nuclear genome from the microsporidian Encephalitozoon intestinalis.
Nat Commun 1:77
D’Hont A, Denoeud F, Aury JM, Baurens FC, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G,
Rouard M, Da Silva C, Jabbari K, Cardi C, Poulain J, Souquet M, Labadie K, Jourda C,
Lengelle J, Rodier-Goud M, Alberti A, Bernard M, Correa M, Ayyampalayam S, McKain MR,
Leebens-Mack J, Burgess D, Freeling M, Mbeguie AMD, Chabannes M, Wicker T, Panaud O,
Barbosa J, Hribova E, Heslop-Harrison P, Habas R, Rivallan R, Francois P, Poiron C, Kilian A,
Burthia D, Jenny C, Bakry F, Brown S, Guignon V, Kema G, Dita M, Waalwijk C, Joseph S,
Dievart A, Jaillon O, Leclercq J, Argout X, Lyons E, Almeida A, Jeridi M, Dolezel J, Roux N,
Risterucci AM, Weissenbach J, Ruiz M, Glaszmann JC, Quetier F, Yahiaoui N, Wincker P
(2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants.
Nature 488(7410):213–217
Dar T-U-H, Ruhman R-U (2017) Occurrence of polyploidy. In: Polyploidy: recent trends and future
perspectives. Springer, New Dehli, pp 31–42
Dassanayake M, Oh DH, Haas JS, Hernandez A, Hong H, Ali S, Yun DJ, Bressan RA, Zhu JK,
Bohnert HJ, Cheeseman JM (2011) The genome of the extremophile crucifer Thellungiella
parvula. Nat Genet 43(9):913–918
de Vries J, Archibald JM (2018) Plant evolution: landmarks on the path to terrestrial life.
New Phytol 217(4):1428–1434
Denker A, De Laat W (2016) The second decade of 3C technologies: detailed insights into nuclear
organization. Genes Dev 30(12):1357–1382
Derelle E, Ferraz C, Rombauts S, Rouze P, Worden AZ, Robbens S, Partensky F, Degroeve S,
Echeynie S, Cooke R, Saeys Y, Wuyts J, Jabbari K, Bowler C, Panaud O, Piegu B, Ball SG, Ral
JP, Bouget FY, Piganeau G, De Baets B, Picard A, Delseny M, Demaille J, Van de Peer Y,
178
D. G. Peterson and M. Arick