Sallet E, Samain S, Samson N, Sanders I, Saurat O, Scarpelli C, Schiex T, Segurens B, Severin
AJ, Sherrier DJ, Shi R, Sims S, Singer SR, Sinharoy S, Sterck L, Viollet A, Wang BB, Wang K,
Wang M, Wang X, Warfsmann J, Weissenbach J, White DD, White JD, Wiley GB, Wincker P,
Xing Y, Yang L, Yao Z, Ying F, Zhai J, Zhou L, Zuber A, Denarie J, Dixon RA, May GD,
Schwartz DC, Rogers J, Quetier F, Town CD, Roe BA (2011) The Medicago genome provides
insight into the evolution of rhizobial symbioses. Nature 480(7378):520–524
Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J,
Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G,
Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, Li T, Wang X, Lu H, Wu T, Zhu M,
Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J,
He S, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Ren X, Chen X,
He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Wang J, Zhao W, Li P,
Chen W, Wang X, Zhang Y, Hu J, Wang J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L,
Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Li G, Liu S, Tao M, Wang J, Zhu L,
Yuan L, Yang H (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica).
Science 296(5565):79–92
Zaharia M, Bolosky WJ, Curtis K, Fox A, Patterson D, Shenker S, Stoica I, Karp RM, Sittler T
(2011) Faster and more accurate sequence alignment with SNAP. arXiv 1111.5572v1:
November 2011
Zdobnov EM, Apweiler R (2001) InterProScan – an integration platform for the signaturerecognition methods in InterPro. Bioinformatics 17(9):847–848
Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn
graphs. Genome Res 18(5):821–829
Zhang J, Carey V, Gentleman R (2003) An extensible application for assembling annotation for
genomic data. Bioinformatics 19(1):155–156
Zhang Q, Chen W, Sun L, Zhao F, Huang B, Yang W, Tao Y, Wang J, Yuan Z, Fan G, Xing Z,
Han C, Pan H, Zhong X, Shi W, Liang X, Du D, Sun F, Xu Z, Hao R, Lv T, Lv Y, Zheng Z,
Sun M, Luo L, Cai M, Gao Y, Wang J, Yin Y, Xu X, Cheng T, Wang J (2012) The genome of
Prunus mume. Nat Commun 3:1318
Zhang T, Hu Y, Jiang W, Fang L, Guan X, Chen J, Zhang J, Saski CA, Scheffler BE, Stelly DM,
Hulse-Kemp AM, Wan Q, Liu B, Liu C, Wang S, Pan M, Wang Y, Wang D, Ye W, Chang L,
Zhang W, Song Q, Kirkbride RC, Chen X, Dennis E, Llewellyn DJ, Peterson DG, Thaxton P,
Jones DC, Wang Q, Xu X, Zhang H, Wu H, Zhou L, Mei G, Chen S, Tian Y, Xiang D, Li X,
Ding J, Zuo Q, Tao L, Liu Y, Li J, Lin Y, Hui Y, Cao Z, Cai C, Zhu X, Jiang Z, Zhou B, Guo W,
Li R, Chen ZJ (2015a) Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1)
provides a resource for fiber improvement. Nat Biotechnol 33(5):531–537
Zhang Y, Zhang S, Liu H, Fu B, Li L, Xie M, Song Y, Li X, Cai J, Wan W, Kui L, Huang H, Lyu J,
Dong Y, Wang W, Huang L, Zhang J, Yang Q, Shan Q, Li Q, Huang W, Tao D, Wang M,
Chen M, Yu Y, Wing RA, Wang W, Hu F (2015b) Genome and comparative transcriptomics of
African wild rice Oryza longistaminata provide insights into molecular mechanism of
rhizomatousness and self-incompatibility. Mol Plant 8(11):1683–1686
Zimin AV, Stevens KA, Crepeau MW, Puiu D, Wegrzyn JL, Yorke JA, Langley CH, Neale DB,
Salzberg SL (2017) An improved assembly of the loblolly pine mega-genome using long-read
single-molecule sequencing. GigaScience 6(1):1–4
Sequencing Plant Genomes
193
AJ, Sherrier DJ, Shi R, Sims S, Singer SR, Sinharoy S, Sterck L, Viollet A, Wang BB, Wang K,
Wang M, Wang X, Warfsmann J, Weissenbach J, White DD, White JD, Wiley GB, Wincker P,
Xing Y, Yang L, Yao Z, Ying F, Zhai J, Zhou L, Zuber A, Denarie J, Dixon RA, May GD,
Schwartz DC, Rogers J, Quetier F, Town CD, Roe BA (2011) The Medicago genome provides
insight into the evolution of rhizobial symbioses. Nature 480(7378):520–524
Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J,
Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G,
Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, Li T, Wang X, Lu H, Wu T, Zhu M,
Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J,
He S, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Ren X, Chen X,
He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Wang J, Zhao W, Li P,
Chen W, Wang X, Zhang Y, Hu J, Wang J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L,
Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Li G, Liu S, Tao M, Wang J, Zhu L,
Yuan L, Yang H (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica).
Science 296(5565):79–92
Zaharia M, Bolosky WJ, Curtis K, Fox A, Patterson D, Shenker S, Stoica I, Karp RM, Sittler T
(2011) Faster and more accurate sequence alignment with SNAP. arXiv 1111.5572v1:
November 2011
Zdobnov EM, Apweiler R (2001) InterProScan – an integration platform for the signaturerecognition methods in InterPro. Bioinformatics 17(9):847–848
Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn
graphs. Genome Res 18(5):821–829
Zhang J, Carey V, Gentleman R (2003) An extensible application for assembling annotation for
genomic data. Bioinformatics 19(1):155–156
Zhang Q, Chen W, Sun L, Zhao F, Huang B, Yang W, Tao Y, Wang J, Yuan Z, Fan G, Xing Z,
Han C, Pan H, Zhong X, Shi W, Liang X, Du D, Sun F, Xu Z, Hao R, Lv T, Lv Y, Zheng Z,
Sun M, Luo L, Cai M, Gao Y, Wang J, Yin Y, Xu X, Cheng T, Wang J (2012) The genome of
Prunus mume. Nat Commun 3:1318
Zhang T, Hu Y, Jiang W, Fang L, Guan X, Chen J, Zhang J, Saski CA, Scheffler BE, Stelly DM,
Hulse-Kemp AM, Wan Q, Liu B, Liu C, Wang S, Pan M, Wang Y, Wang D, Ye W, Chang L,
Zhang W, Song Q, Kirkbride RC, Chen X, Dennis E, Llewellyn DJ, Peterson DG, Thaxton P,
Jones DC, Wang Q, Xu X, Zhang H, Wu H, Zhou L, Mei G, Chen S, Tian Y, Xiang D, Li X,
Ding J, Zuo Q, Tao L, Liu Y, Li J, Lin Y, Hui Y, Cao Z, Cai C, Zhu X, Jiang Z, Zhou B, Guo W,
Li R, Chen ZJ (2015a) Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1)
provides a resource for fiber improvement. Nat Biotechnol 33(5):531–537
Zhang Y, Zhang S, Liu H, Fu B, Li L, Xie M, Song Y, Li X, Cai J, Wan W, Kui L, Huang H, Lyu J,
Dong Y, Wang W, Huang L, Zhang J, Yang Q, Shan Q, Li Q, Huang W, Tao D, Wang M,
Chen M, Yu Y, Wing RA, Wang W, Hu F (2015b) Genome and comparative transcriptomics of
African wild rice Oryza longistaminata provide insights into molecular mechanism of
rhizomatousness and self-incompatibility. Mol Plant 8(11):1683–1686
Zimin AV, Stevens KA, Crepeau MW, Puiu D, Wegrzyn JL, Yorke JA, Langley CH, Neale DB,
Salzberg SL (2017) An improved assembly of the loblolly pine mega-genome using long-read
single-molecule sequencing. GigaScience 6(1):1–4
Sequencing Plant Genomes
193