| Reference publication |
|
1. Huang, S., Ding, J., Deng, D., Tang, W., Sun, H., Liu,
D., ... & Yu, J. (2013). Draft genome of the kiwifruit
Actinidia chinensis. Nature communications, 4(1), 1-9. |
|
2. Jia, J., Zhao, S., Kong, X., Li, Y., Zhao, G., He, W.,
... & Jing, R. (2013). Aegilops tauschii draft genome
sequence reveals a gene repertoire for wheat adaptation.
Nature , 496(7443), 91-95. |
|
3. Mérai, Z., Graeber, K., Wilhelmsson, P., Ullrich, K. K.,
Arshad, W., Grosche, C., ... & Leubner-Metzger, G. (2019).
Aethionema arabicum: a novel model plant to study the light
control of seed germination. Journal of experimental botany,
70(12), 3313-3328. |
|
4. Griesmann, M., Chang, Y., Liu, X., Song, Y., Haberer, G.,
Crook, M. B., ... & Roswanjaya, Y. P. (2018). Phylogenomics
reveals multiple losses of nitrogen-fixing root nodule
symbiosis. Science, 361(6398), eaat1743. |
|
5. Clouse, J. W., Adhikary, D., Page, J. T., Ramaraj, T.,
Deyholos, M. K., Udall, J. A., ... & Maughan, P. J. (2016).
The amaranth genome: genome, transcriptome, and physical map
assembly. The Plant Genome, 9(1). |
|
6. Albert, V. A., Barbazuk, W. B., Depamphilis, C. W., Der,
J. P., Leebens-Mack, J., Ma, H., ... & Soltis, D. E. (2013).
The Amborella genome and the evolution of flowering plants.
Science, 342(6165), 1241089. |
|
7. Ming, R., VanBuren, R., Wai, C. M., Tang, H., Schatz, M.
C., Bowers, J. E., ... & Zhang, J. (2015). The pineapple
genome and the evolution of CAM photosynthesis. Nature
genetics, 47(12), 1435-1442. |
|
8. Li, M., Zhang, D., Gao, Q., Luo, Y., Zhang, H., Ma, B.,
... & Li, Q. (2019). Genome structure and evolution of
Antirrhinum majus L. Nature plants, 5(2), 174-183. |
|
9. Filiault, D. L., Ballerini, E. S., Mandakova, T., Aköz,
G., Derieg, N. J., Schmutz, J., ... & Hellsten, U. (2018).
The Aquilegia genome provides insight into adaptive
radiation and reveals an extraordinarily polymorphic
chromosome with a unique history. Elife, 7, e36426. |
|
10. Hu, T. T., Pattyn, P., Bakker, E. G., Cao, J., Cheng, J.
F., Clark, R. M., ... & Haberer, G. (2011). The Arabidopsis
lyrata genome sequence and the basis of rapid genome size
change. Nature genetics, 43(5), 476. |
|
11. Cheng, C. Y., Krishnakumar, V., Chan, A. P.,
Thibaud-Nissen, F., Schobel, S., & Town, C. D. (2017).
Araport11: a complete reannotation of the Arabidopsis
thaliana reference genome. The Plant Journal, 89(4),
789-804. |
|
12. Bertioli, D. J., Cannon, S. B., Froenicke, L., Huang,
G., Farmer, A. D., Cannon, E. K., ... & Ren, L. (2016). The
genome sequences of Arachis duranensis and Arachis ipaensis,
the diploid ancestors of cultivated peanut. Nature
genetics, 48(4), 438. |
|
13. Gardner, E. M., Johnson, M. G., Ragone, D., Wickett, N.
J., & Zerega, N. J. (2016). Low-coverage, whole-genome
sequencing of Artocarpus camansi (Moraceae) for phylogenetic
marker development and gene discovery. Applications in Plant
Sciences, 4(7), 1600017. |
|
14. Harkess, A., Zhou, J., Xu, C., Bowers, J. E., Van der
Hulst, R., Ayyampalayam, S., ... & Tang, H. (2017). The
asparagus genome sheds light on the origin and evolution of
a young Y chromosome. Nature communications, 8(1), 1-10. |
|
15. Wang, X., Xu, Y., Zhang, S., Cao, L., Huang, Y., Cheng,
J., ... & Yu, H. (2017). Genomic analyses of primitive, wild
and cultivated citrus provide insights into asexual
reproduction. Nature genetics, 49(5), 765. |
|
16. Li, F. W., Brouwer, P., Carretero-Paulet, L., Cheng, S.,
De Vries, J., Delaux, P. M., ... & Simenc, M. (2018). Fern
genomes elucidate land plant evolution and cyanobacterial
symbioses. Nature plants, 4(7), 460-472. |
|
17. Xie, D., Xu, Y., Wang, J., Liu, W., Zhou, Q., Luo, S.,
... & Yang, X. (2019). The wax gourd genomes offer insights
into the genetic diversity and ancestral cucurbit karyotype.
Nature communications, 10(1), 1-12. |
|
18. Dohm, J. C., Minoche, A. E., Holtgräwe, D.,
Capella-Gutiérrez, S., Zakrzewski, F., Tafer, H., ... &
Goesmann, A. (2014). The genome of the recently domesticated
crop plant sugar beet (Beta vulgaris). Nature, 505(7484),
546-549. |
|
19. Salojärvi, J., Smolander, O. P., Nieminen, K.,
Rajaraman, S., Safronov, O., Safdari, P., ... & Rastas, P.
(2017). Genome sequencing and population genomic analyses
provide insights into the adaptive landscape of silver
birch. Nature genetics, 49(6), 904-912. |
|
20. International Brachypodium Initiative. (2010). Genome
sequencing and analysis of the model grass Brachypodium
distachyon. Nature, 463(7282), 763. |
|
21. Yang, J., Liu, D., Wang, X., Ji, C., Cheng, F., Liu, B.,
... & Yao, P. (2016). The genome sequence of allopolyploid
Brassica juncea and analysis of differential homoeolog gene
expression influencing selection. Nature genetics, 48(10),
1225. |
|
22. Chalhoub, B., Denoeud, F., Liu, S., Parkin, I. A., Tang,
H., Wang, X., ... & Corréa, M. (2014). Early allopolyploid
evolution in the post-Neolithic Brassica napus oilseed
genome. Science, 345(6199), 950-953. |
|
23. Liu, S., Liu, Y., Yang, X., Tong, C., Edwards, D.,
Parkin, I. A., ... & Wang, X. (2014). The Brassica oleracea
genome reveals the asymmetrical evolution of polyploid
genomes. Nature communications, 5, 3930. |
|
24. Parkin, I. A., Koh, C., Tang, H., Robinson, S. J.,
Kagale, S., Clarke, W. E., ... & Denoeud, F. (2014).
Transcriptome and methylome profiling reveals relics of
genome dominance in the mesopolyploid Brassica oleracea.
Genome biology, 15(6), R77. |
|
25. Wang, X., Wang, H., Wang, J., Sun, R., Wu, J., Liu, S.,
... & Huang, S. (2011). The genome of the mesopolyploid crop
species Brassica rapa. Nature genetics, 43(10), 1035. |
|
26. Varshney, R. K., Chen, W., Li, Y., Bharti, A. K.,
Saxena, R. K., Schlueter, J. A., ... & Farmer, A. D. (2012).
Draft genome sequence of pigeonpea (Cajanus cajan), an
orphan legume crop of resource-poor farmers. Nature
biotechnology, 30(1), 83. |
|
27. Hoopes, G. M., Hamilton, J. P., Kim, J., Zhao, D.,
Wiegert-Rininger, K., Crisovan, E., & Buell, C. R. (2018).
Genome assembly and annotation of the medicinal plant
Calotropis gigantea, a producer of anticancer and
antimalarial cardenolides. G3: Genes, Genomes, Genetics,
8(2), 385-391. |
|
28. Xia, E. H., Zhang, H. B., Sheng, J., Li, K., Zhang, Q.
J., Kim, C., ... & Huang, H. (2017). The tea tree genome
provides insights into tea flavor and independent evolution
of caffeine biosynthesis. Molecular plant, 10(6), 866-877. |
|
29. Kagale, S., Koh, C., Nixon, J., Bollina, V., Clarke, W.
E., Tuteja, R., ... & Higgins, E. E. (2014). The emerging
biofuel crop Camelina sativa retains a highly
undifferentiated hexaploid genome structure. Nature
communications, 5(1), 1-11. |
|
30. Kasianov, A. S., Klepikova, A. V., Kulakovskiy, I. V.,
Gerasimov, E. S., Fedotova, A. V., Besedina, E. G., ... &
Penin, A. A. (2017). High-quality genome assembly of
Capsella bursa-pastoris reveals asymmetry of regulatory
elements at early stages of polyploid genome evolution.
The
Plant Journal, 91(2), 278-291. |
|
31. Slotte, T., Hazzouri, K. M., Ågren, J. A., Koenig, D.,
Maumus, F., Guo, Y. L., ... & Wang, W. (2013). The Capsella
rubella genome and the genomic consequences of rapid mating
system evolution. Nature genetics, 45(7), 831-835. |
|
32. Qin, C., Yu, C., Shen, Y., Fang, X., Chen, L., Min, J.,
... & Yang, Y. (2014). Whole-genome sequencing of cultivated
and wild peppers provides insights into Capsicum
domestication and specialization. Proceedings of the
National Academy of Sciences, 111(14), 5135-5140. |
|
33. Kim, S., Park, J., Yeom, S. I., Kim, Y. M., Seo, E.,
Kim, K. T., ... & Kim, S. B. (2017). New reference genome
sequences of hot pepper reveal the massive evolution of
plant disease-resistance genes by retroduplication. Genome
biology, 18(1), 210. |
|
34. Gan, X., Hay, A., Kwantes, M., Haberer, G., Hallab, A.,
Ioio, R. D., ... & Nikolov, L. A. (2016). The Cardamine
hirsuta genome offers insight into the evolution of
morphological diversity. Nature plants, 2(11), 1-7. |
|
35. Ming, R., Hou, S., Feng, Y., Yu, Q., Dionne-Laporte, A.,
Saw, J. H., ... & Salzberg, S. L. (2008). The draft genome
of the transgenic tropical fruit tree papaya (Carica papaya
Linnaeus). Nature, 452(7190), 991-996. |
|
36. Huang, Y., Xiao, L., Zhang, Z., Zhang, R., Wang, Z.,
Huang, C., ... & Shen, C. (2019). The genomes of pecan and
Chinese hickory provide insights into Carya evolution and
nut nutrition. GigaScience, 8(5), giz036. |
|
37. Fukushima, K., Fang, X., Alvarez-Ponce, D., Cai, H.,
Carretero-Paulet, L., Chen, C., ... & Hoshi, Y. (2017).
Genome of the pitcher plant Cephalotus reveals genetic
changes associated with carnivory. Nature ecology &
evolution, 1(3), 0059. |
|
38. Nishiyama, T., Sakayama, H., De Vries, J., Buschmann,
H., Saint-Marcoux, D., Ullrich, K. K., ... & Vosolsobe, S.
(2018). The Chara genome: secondary complexity and
implications for plant terrestrialization. Cell, 174(2),
448-464. |
|
39. Yasui, Y., Hirakawa, H., Oikawa, T., Toyoshima, M.,
Matsuzaki, C., Ueno, M., ... & Tanaka, K. (2016). Draft
genome sequence of an inbred line of Chenopodium quinoa, an
allotetraploid crop with great environmental adaptability
and outstanding nutritional properties. DNA Research, 23(6),
535-546. |
|
40. Merchant, S. S., Prochnik, S. E., Vallon, O., Harris, E.
H., Karpowicz, S. J., Witman, G. B., ... & Marshall, W. F.
(2007). The Chlamydomonas genome reveals the evolution of
key animal and plant functions. Science, 318(5848), 245-250. |
|
41. Roth, M. S., Cokus, S. J., Gallaher, S. D., Walter, A.,
Lopez, D., Erickson, E., ... & Pellegrini, M. (2017).
Chromosome-level genome assembly and transcriptome of the
green alga Chromochloris zofingiensis illuminates
astaxanthin production. Proceedings of the National Academy
of Sciences, 114(21), E4296-E4305. |
|
42. Song, C., Liu, Y., Song, A., Dong, G., Zhao, H., Sun,
W., ... & Niu, Y. (2018). The Chrysanthemum nankingense
genome provides insights into the evolution and
diversification of chrysanthemum flowers and medicinal
traits. Molecular plant, 11(12), 1482-1491. |
|
43. Varshney, R. K., Song, C., Saxena, R. K., Azam, S., Yu,
S., Sharpe, A. G., ... & Millan, T. (2013). Draft genome
sequence of chickpea (Cicer arietinum) provides a resource
for trait improvement. Nature biotechnology, 31(3), 240. |
|
44. Guo, S., Zhang, J., Sun, H., Salse, J., Lucas, W. J.,
Zhang, H., ... & Min, J. (2013). The draft genome of
watermelon (Citrullus lanatus) and resequencing of 20
diverse accessions. Nature genetics, 45(1), 51-58. |
|
45. Wu S, Wang X, Reddy U, Sun H, Bao K, Gao L, Mao L, Patel
T, Ortiz C, Abburi VL, Nimmakayala P, Branham S, Wechter P,
Massey L, Ling KS, Kousik C, Hammar SA, Tadmor Y, Portnoy V,
Gur A, Katzir N, Guner N, Davis A, Hernandez AG, Wright CL,
McGregor C, Jarret R, Zhang X, Xu Y, Wehner TC, Grumet R,
Levi A, Fei Z (2019) Genome of 'Charleston Gray', the
principal American watermelon cultivar, and genetic
characterization of 1,365 accessions in the U.S. National
Plant Germplasm System watermelon collection. Plant
Biotechnol J |
|
46. Wu, G. A., Prochnik, S., Jenkins, J., Salse, J.,
Hellsten, U., Murat, F., ... & Takita, M. A. (2014).
Sequencing of diverse mandarin, pummelo and orange genomes
reveals complex history of admixture during citrus
domestication. Nature biotechnology, 32(7), 656-662. |
|
47. Xu, Q., Chen, L. L., Ruan, X., Chen, D., Zhu, A., Chen,
C., ... & Chen, J. (2013). The draft genome of sweet orange
(Citrus sinensis). Nature genetics, 45(1), 59. |
|
48. Shimizu, T., Tanizawa, Y., Mochizuki, T., Nagasaki, H.,
Yoshioka, T., Toyoda, A., ... & Nakamura, Y. (2017). Draft
sequencing of the heterozygous diploid genome of satsuma
(Citrus unshiu Marc.) using a hybrid assembly approach.
Frontiers in genetics, 8, 180. |
|
49. Denoeud, F., Carretero-Paulet, L., Dereeper, A., Droc,
G., Guyot, R., Pietrella, M., ... & Aury, J. M. (2014). The
coffee genome provides insight into the convergent evolution
of caffeine biosynthesis. Science, 345(6201), 1181-1184. |
|
50. Garcia-Mas, J., Benjak, A., Sanseverino, W., Bourgeois,
M., Mir, G., González, V. M., ... & Alioto, T. (2012). The
genome of melon (Cucumis melo L.). Proceedings of the
National Academy of Sciences, 109(29), 11872-11877. |
|
51. Li, Q., Li, H., Huang, W., Xu, Y., Zhou, Q., Wang, S.,
... & Zhang, Z. (2019). A chromosome-scale genome assembly
of cucumber (Cucumis sativus L.). GigaScience, 8(6),
giz072. |
|
52. Qi, J., Liu, X., Shen, D., Miao, H., Xie, B., Li, X.,
... & Du, Y. (2013). A genomic variation map provides
insights into the genetic basis of cucumber domestication
and diversity. Nature genetics, 45(12), 1510. |
|
53. Barrera-Redondo, J., Ibarra-Laclette, E., Vázquez-Lobo,
A., Gutiérrez-Guerrero, Y. T., de la Vega, G. S., Piñero,
D., ... & Eguiarte, L. E. (2019). The genome of Cucurbita
argyrosperma (silver-seed gourd) reveals faster rates of
protein-coding gene and long noncoding RNA turnover and
neofunctionalization within Cucurbita. Molecular plant,
12(4), 506-520. |
|
54. Sun, H., Wu, S., Zhang, G., Jiao, C., Guo, S., Ren, Y.,
... & Zhang, F. (2017). Karyotype stability and unbiased
fractionation in the paleo-allotetraploid Cucurbita genomes.
Molecular plant, 10(10), 1293-1306. |
|
55. Montero-Pau, J., Blanca, J., Bombarely, A., Ziarsolo,
P., Esteras, C., Martí-Gómez, C., ... & Picó, B. (2018). De
novo assembly of the zucchini genome reveals a whole-genome
duplication associated with the origin of the Cucurbita
genus. Plant biotechnology journal, 16(6), 1161-1171. |
|
56. Sun, G., Xu, Y., Liu, H., Sun, T., Zhang, J.,
Hettenhausen, C., ... & Wang, L. (2018). Large-scale gene
losses underlie the genome evolution of parasitic plant
Cuscuta australis. Nature communications, 9(1), 1-8. |
|
57. Vogel, A., Schwacke, R., Denton, A. K., Usadel, B.,
Hollmann, J., Fischer, K., ... & Mayer, K. F. (2018).
Footprints of parasitism in the genome of the parasitic
flowering plant Cuscuta campestris. Nature communications,
9(1), 1-11. |
|
58. Iorizzo, M., Ellison, S., Senalik, D., Zeng, P.,
Satapoomin, P., Huang, J., ... & Yildiz, M. (2016). A
high-quality carrot genome assembly provides new insights
into carotenoid accumulation and asterid genome evolution.
Nature genetics, 48(6), 657. |
|
59. Yagi, M. A. S. A. F. U. M. I., Kosugi, S. H. U. N. I. C.
H. I., Hirakawa, H. I. D. E. K. I., Ohmiya, A. K. E. M. I.,
Tanase, K. O. J. I., Harada, T. A. R. O., ... & Yamaguchi,
H. I. R. O. Y. A. S. U. (2014). Sequence analysis of the
genome of carnation (Dianthus caryophyllus L.). DNA
Research, 21(3), 231-241. |
|
60. Guo, L., Qiu, J., Ye, C., Jin, G., Mao, L., Zhang, H.,
... & Lin, Z. (2017). Echinochloa crus-galli genome analysis
provides insight into its adaptation and invasiveness as a
weed. Nature communications, 8(1), 1-10. |
|
61. Cock, J. M., Sterck, L., Rouzé, P., Scornet, D., Allen,
A. E., Amoutzias, G., ... & Beszteri, B. (2010). The
Ectocarpus genome and the independent evolution of
multicellularity in brown algae. Nature, 465(7298),
617-621. |
|
62. Wuyun, T. N., Wang, L., Liu, H., Wang, X., Zhang, L.,
Bennetzen, J. L., ... & Wang, L. (2018). The hardy rubber
tree genome provides insights into the evolution of
polyisoprene biosynthesis. Molecular plant, 11(3), 429-442. |
|
63. Yang, R., Jarvis, D. J., Chen, H., Beilstein, M.,
Grimwood, J., Jenkins, J., ... & Schmutz, J. (2013). The
reference genome of the halophytic plant Eutrema
salsugineum. Frontiers in Plant Science, 4, 46. |
|
64. Yasui, Y., Hirakawa, H., Ueno, M., Matsui, K.,
Katsube-Tanaka, T., Yang, S. J., ... & Mori, M. (2016).
Assembly of the draft genome of buckwheat and its
applications in identifying agronomically useful genes.
DNA
Research, 23(3), 215-224. |
|
65. Zhang, L., Li, X., Ma, B., Gao, Q., Du, H., Han, Y., ...
& Lu, H. (2017). The tartary buckwheat genome provides
insights into rutin biosynthesis and abiotic stress
tolerance. Molecular plant, 10(9), 1224-1237. |
|
66. Chang, Y., Liu, H., Liu, M., Liao, X., Sahu, S. K., Fu,
Y., ... & Hendre, P. S. (2019). The draft genomes of five
agriculturally important African orphan crops. GigaScience,
8(3), giy152. |
|
67. Edger, P. P., Poorten, T. J., VanBuren, R., Hardigan, M.
A., Colle, M., McKain, M. R., ... & Alger, E. I. (2019).
Origin and evolution of the octoploid strawberry genome.
Nature genetics, 51(3), 541-547. |
|
68. Shulaev, V., Sargent, D. J., Crowhurst, R. N., Mockler,
T. C., Folkerts, O., Delcher, A. L., ... & Burns, P. (2011).
The genome of woodland strawberry (Fragaria vesca). Nature
genetics, 43(2), 109. |
|
69. Sollars, E. S., Harper, A. L., Kelly, L. J., Sambles, C.
M., Ramirez-Gonzalez, R. H., Swarbreck, D., ... & Worswick,
G. (2017). Genome sequence and genetic diversity of European
ash trees. Nature, 541(7636), 212-216. |
|
70. Schmutz, J., Cannon, S. B., Schlueter, J., Ma, J.,
Mitros, T., Nelson, W., ... & Xu, D. (2010). Genome sequence
of the palaeopolyploid soybean. Nature, 463(7278), 178-183. |
|
71. Mochida, K., Sakurai, T., Seki, H., Yoshida, T.,
Takahagi, K., Sawai, S., ... & Saito, K. (2017). Draft
genome assembly and annotation of Glycyrrhiza uralensis, a
medicinal legume. The Plant Journal, 89(2), 181-194. |
|
72. Li, F., Fan, G., Wang, K., Sun, F., Yuan, Y., Song, G.,
... & Chen, W. (2014). Genome sequence of the cultivated
cotton Gossypium arboreum. Nature genetics, 46(6), 567-572. |
|
73. Wang, M., Tu, L., Yuan, D., Zhu, D., Shen, C., Li, J.,
... & Ye, Z. (2019). Reference genome sequences of two
cultivated allotetraploid cottons, Gossypium hirsutum and
Gossypium barbadense. Nature genetics, 51(2), 224-229. |
|
74. Wang, K., Wang, Z., Li, F., Ye, W., Wang, J., Song, G.,
... & Zou, C. (2012). The draft genome of a diploid cotton
Gossypium raimondii. Nature genetics, 44(10), 1098-1103. |
|
75. Silva-Junior, O. B., Grattapaglia, D., Novaes, E., &
Collevatti, R. G. (2018). Genome assembly of the Pink Ipê
(Handroanthus impetiginosus, Bignoniaceae), a highly valued,
ecologically keystone Neotropical timber forest tree.
GigaScience, 7(1), gix125. |
|
76. Badouin, H., Gouzy, J., Grassa, C. J., Murat, F.,
Staton, S. E., Cottret, L., ... & Legrand, L. (2017). The
sunflower genome provides insights into oil metabolism,
flowering and Asterid evolution. Nature, 546(7656),
148-152. |
|
77. Mascher, M., Gundlach, H., Himmelbach, A., Beier, S.,
Twardziok, S. O., Wicker, T., ... & Bayer, M. (2017). A
chromosome conformation capture ordered sequence of the
barley genome. Nature, 544(7651), 427-433. |
|
78. Wu, S., Lau, K. H., Cao, Q., Hamilton, J. P., Sun, H.,
Zhou, C., ... & Crisovan, E. (2018). Genome sequences of two
diploid wild relatives of cultivated sweetpotato reveal
targets for genetic improvement. Nature communications,
9(1), 1-12. |
|
79. Martínez-García, P. J., Crepeau, M. W., Puiu, D.,
Gonzalez-Ibeas, D., Whalen, J., Stevens, K. A., ... &
Chakraborty, S. (2016). The walnut (Juglans regia) genome
sequence reveals diversity in genes coding for the
biosynthesis of non-structural polyphenols. The Plant
Journal, 87(5), 507-532. |
|
80. Yang, X., Hu, R., Yin, H., Jenkins, J., Shu, S., Tang,
H., ... & Heyduk, K. (2017). The Kalanchoë genome provides
insights into convergent evolution and building blocks of
crassulacean acid metabolism. Nature communications, 8(1),
1-15. |
|
81. Wu, S., Shamimuzzaman, M., Sun, H., Salse, J., Sui, X.,
Wilder, A., ... & Fei, Z. (2017). The bottle gourd genome
provides insights into Cucurbitaceae evolution and
facilitates mapping of a Papaya ring-spot virus resistance
locus. The Plant Journal, 92(5), 963-975. |
|
82. Haudry, A., Platts, A. E., Vello, E., Hoen, D. R.,
Leclercq, M., Williamson, R. J., ... & Dewar, K. (2013). An
atlas of over 90,000 conserved noncoding sequences provides
insight into crucifer regulatory regions. Nature genetics,
45(8), 891-898. |
|
83. Wang, Z., Hobson, N., Galindo, L., Zhu, S., Shi, D.,
McDill, J., ... & Lambert, G. (2012). The genome of flax
(Linum usitatissimum) assembled de novo from short shotgun
sequence reads. The Plant Journal, 72(3), 461-473. |
|
84. Chen, J., Hao, Z., Guang, X., Zhao, C., Wang, P., Xue,
L., ... & Xu, H. (2019). Liriodendron genome sheds light on
angiosperm phylogeny and species–pair differentiation.
Nature plants, 5(1), 18-25. |
|
85. Sato, S., Nakamura, Y., Kaneko, T., Asamizu, E., Kato,
T., Nakao, M., ... & Fujishiro, T. (2008). Genome structure
of the legume, Lotus japonicus. DNA Research, 15(4),
227-239. |
|
86. Velasco, R., Zharkikh, A., Affourtit, J., Dhingra, A.,
Cestaro, A., Kalyanaraman, A., ... & Salvi, S. (2010). The
genome of the domesticated apple (Malus× domestica Borkh.).
Nature genetics, 42(10), 833-839. |
|
87. Bredeson, J. V., Lyons, J. B., Prochnik, S. E., Wu, G.
A., Ha, C. M., Edsinger-Gonzales, E., ... & Nauluvula, P.
(2016). Sequencing wild and cultivated cassava and related
species reveals extensive interspecific hybridization and
genetic diversity. Nature biotechnology, 34(5), 562. |
|
88. Bowman, J. L., Kohchi, T., Yamato, K. T., Jenkins, J.,
Shu, S., Ishizaki, K., ... & Adam, C. (2017). Insights into
land plant evolution garnered from the Marchantia polymorpha
genome. Cell, 171(2), 287-304. |
|
89. Tang, H., Krishnakumar, V., Bidwell, S., Rosen, B.,
Chan, A., Zhou, S., ... & Mayer, K. F. (2014). An improved
genome release (version Mt4. 0) for the model legume
Medicago truncatula. BMC genomics, 15(1), 312. |
|
90. D’hont, A., Denoeud, F., Aury, J. M., Baurens, F. C.,
Carreel, F., Garsmeur, O., ... & Da Silva, C. (2012). The
banana (Musa acuminata) genome and the evolution of
monocotyledonous plants. Nature, 488(7410), 213-217. |
|
91. Wang, Z., Miao, H., Liu, J., Xu, B., Yao, X., Xu, C.,
... & Zhang, J. (2019). Musa balbisiana genome reveals
subgenome evolution and functional divergence. Nature
plants, 5(8), 810-821. |
|
92. Davey, M. W., Gudimella, R., Harikrishna, J. A., Sin, L.
W., Khalid, N., & Keulemans, J. (2013). A draft Musa
balbisiana genome sequence for molecular genetics in
polyploid, inter-and intra-specific Musa hybrids. BMC
genomics, 14(1), 683. |
|
93. Wu, W., Yang, Y. L., He, W. M., Rouard, M., Li, W. M.,
Xu, M., ... & Ge, X. J. (2016). Whole genome sequencing of a
banana wild relative Musa itinerans provides insights into
lineage-specific diversification of the Musa genus.
Scientific reports, 6, 31586. |
|
94. Belser, C., Istace, B., Denis, E., Dubarry, M., Baurens,
F. C., Falentin, C., ... & Deniot, G. (2018).
Chromosome-scale assemblies of plant genomes using nanopore
long reads and optical maps. Nature plants, 4(11), 879-887. |
|
95. Xu, S., Brockmöller, T., Navarro-Quezada, A., Kuhl, H.,
Gase, K., Ling, Z., ... & Lyons, E. (2017). Wild tobacco
genomes reveal the evolution of nicotine biosynthesis.
Proceedings of the National Academy of Sciences, 114(23),
6133-6138. |
|
96. Bombarely, A., Rosli, H. G., Vrebalov, J., Moffett, P.,
Mueller, L. A., & Martin, G. B. (2012). A draft genome
sequence of Nicotiana benthamiana to enhance molecular
plant-microbe biology research. Molecular Plant-Microbe
Interactions, 25(12), 1523-1530. |
|
97. Unver, T., Wu, Z., Sterck, L., Turktas, M., Lohaus, R.,
Li, Z., ... & Llorens, C. (2017). Genome of wild olive and
the evolution of oil biosynthesis. Proceedings of the
National Academy of Sciences, 114(44), E9413-E9422. |
|
98. VanBuren, R., Bryant, D., Edger, P. P., Tang, H.,
Burgess, D., Challabathula, D., ... & Freeling, M. (2015).
Single-molecule sequencing of the desiccation-tolerant grass
Oropetium thomaeum. Nature, 527(7579), 508-511. |
|
99. Stein, J. C., Yu, Y., Copetti, D., Zwickl, D. J., Zhang,
L., Zhang, C., ... & Wei, S. (2018). Genomes of 13
domesticated and wild rice relatives highlight genetic
conservation, turnover and innovation across the genus
Oryza. Nature genetics, 50(2), 285-296. |
|
100. Chen, J., Huang, Q., Gao, D., Wang, J., Lang, Y., Liu,
T., ... & Chen, C. (2013). Whole-genome sequencing of Oryza
brachyantha reveals mechanisms underlying Oryza genome
evolution. Nature communications, 4(1), 1-9. |
|
101. Wang, M., Yu, Y., Haberer, G., Marri, P. R., Fan, C.,
Goicoechea, J. L., ... & Cossu, R. M. (2014). The genome
sequence of African rice (Oryza glaberrima) and evidence for
independent domestication. Nature genetics, 46(9), 982-988. |
|
102. Zhang, Y., Zhang, S., Liu, H., Fu, B., Li, L., Xie, M.,
... & Kui, L. (2015). Genome and comparative transcriptomics
of African wild rice Oryza longistaminata provide insights
into molecular mechanism of rhizomatousness and
self-incompatibility. Molecular plant, 8(11), 1683-1686. |
|
103. Yu, J., Hu, S., Wang, J., Wong, G. K. S., Li, S., Liu,
B., ... & Cao, M. (2002). A draft sequence of the rice
genome (Oryza sativa L. ssp. indica). Science, 296(5565),
79-92. |
|
104. Goff, S. A., Ricke, D., Lan, T. H., Presting, G., Wang,
R., Dunn, M., ... & Hadley, D. (2002). A draft sequence of
the rice genome (Oryza sativa L. ssp. japonica). Science,
296(5565), 92-100. |
|
105. Palenik, B., Grimwood, J., Aerts, A., Rouzé, P.,
Salamov, A., Putnam, N., ... & Zhou, K. (2007). The tiny
eukaryote Ostreococcus provides genomic insights into the
paradox of plankton speciation. Proceedings of the National
Academy of Sciences, 104(18), 7705-7710. |
|
106. Zhang, D., Li, W., Xia, E. H., Zhang, Q. J., Liu, Y.,
Zhang, Y., ... & Gao, L. Z. (2017). The medicinal herb Panax
notoginseng genome provides insights into ginsenoside
biosynthesis and genome evolution. Molecular plant, 10(6),
903-907. |
|
107. Bombarely, A., Moser, M., Amrad, A., Bao, M., Bapaume,
L., Barry, C. S., ... & Bucher, M. (2016). Insight into the
evolution of the Solanaceae from the parental genomes of
Petunia hybrida. Nature plants, 2(6), 16074. |
|
108. Bowler, C., Allen, A. E., Badger, J. H., Grimwood, J.,
Jabbari, K., Kuo, A., ... & Rayko, E. (2008). The
Phaeodactylum genome reveals the evolutionary history of
diatom genomes. Nature, 456(7219), 239. |
|
109. Chao, Y. T., Chen, W. C., Chen, C. Y., Ho, H. Y., Yeh,
C. H., Kuo, Y. T., ... & Hsu, H. L. (2018). Chromosome-level
assembly, genetic and physical mapping of Phalaenopsis
aphrodite genome provides new insights into species
adaptation and resources for orchid breeding. Plant
biotechnology journal, 16(12), 2027-2041. |
|
110. Cai, J., Liu, X., Vanneste, K., Proost, S., Tsai, W.
C., Liu, K. W., ... & Zheng, Z. (2015). The genome sequence
of the orchid Phalaenopsis equestris. Nature genetics,
47(1), 65-72. |
|
111. Schmutz, J., McClean, P. E., Mamidi, S., Wu, G. A.,
Cannon, S. B., Grimwood, J., ... & Torres-Torres, M. (2014).
A reference genome for common bean and genome-wide analysis
of dual domestications. Nature genetics, 46(7), 707. |
|
112. Al-Mssallem, I. S., Hu, S., Zhang, X., Lin, Q., Liu,
W., Tan, J., ... & Yin, Y. (2013). Genome sequence of the
date palm Phoenix dactylifera L. Nature communications, 4,
2274. |
|
113. Lang, D., Ullrich, K. K., Murat, F., Fuchs, J.,
Jenkins, J., Haas, F. B., ... & Vives, C. (2018). The
Physcomitrella patens chromosome-scale assembly reveals moss
genome structure and evolution. The Plant Journal, 93(3),
515-533. |
|
114. Nystedt, B., Street, N. R., Wetterbom, A., Zuccolo, A.,
Lin, Y. C., Scofield, D. G., ... & Vicedomini, R. (2013).
The Norway spruce genome sequence and conifer genome
evolution. Nature, 497(7451), 579-584. |
|
115. Ma, J., Wan, D., Duan, B., Bai, X., Bai, Q., Chen, N.,
& Ma, T. (2019). Genome sequence and genetic transformation
of a widely distributed and cultivated poplar. Plant
biotechnology journal, 17(2), 451-460. |
|
116. Ma, T., Wang, J., Zhou, G., Yue, Z., Hu, Q., Chen, Y.,
... & Wang, K. (2013). Genomic insights into salt adaptation
in a desert poplar. Nature communications, 4(1), 1-9. |
|
117. Yang, W., Wang, K., Zhang, J., Ma, J., Liu, J., & Ma,
T. (2017). The draft genome sequence of a desert tree
Populus pruinosa. GigaScience, 6(9), gix075. |
|
118. Lin, Y. C., Wang, J., Delhomme, N., Schiffthaler, B.,
Sundström, G., Zuccolo, A., ... & Hoeppner, M. P. (2018).
Functional and evolutionary genomic inferences in Populus
through genome and population sequencing of American and
European aspen. Proceedings of the National Academy of
Sciences, 115(46), E10970-E10978. |
|
119. Tuskan, G. A., DiFazio, S., Jansson, S., Bohlmann, J.,
Grigoriev, I., Hellsten, U., ... & Schein, J. (2006). The
genome of black cottonwood, Populus trichocarpa (Torr. &
Gray). Science, 313(5793), 1596-1604. |
|
120. Brawley, S. H., Blouin, N. A., Ficko-Blean, E.,
Wheeler, G. L., Lohr, M., Goodson, H. V., ... & Marriage, T.
N. (2017). Insights into the red algae and eukaryotic
evolution from the genome of Porphyra umbilicalis
(Bangiophyceae, Rhodophyta). Proceedings of the National
Academy of Sciences, 114(31), E6361-E6370. |
|
121. Cocker, J. M., Wright, J., Li, J., Swarbreck, D., Dyer,
S., Caccamo, M., & Gilmartin, P. M. (2018). Primula vulgaris
(primrose) genome assembly, annotation and gene expression,
with comparative genomics on the heterostyly supergene.
Scientific reports, 8(1), 1-13. |
|
122. Shirasawa, K., Isuzugawa, K., Ikenaga, M., Saito, Y.,
Yamamoto, T., Hirakawa, H., & Isobe, S. (2017). The genome
sequence of sweet cherry (Prunus avium) for use in
genomics-assisted breeding. DNA Research, 24(5), 499-508. |
|
123. Zhang, Q., Chen, W., Sun, L., Zhao, F., Huang, B.,
Yang, W., ... & Xing, Z. (2012). The genome of Prunus mume.
Nature communications, 3(1), 1-8. |
|
124. Verde, I., Abbott, A. G., Scalabrin, S., Jung, S., Shu,
S., Marroni, F., ... & Zuccolo, A. (2013). The high-quality
draft genome of peach (Prunus persica) identifies unique
patterns of genetic diversity, domestication and genome
evolution. Nature genetics, 45(5), 487. |
|
125. Wu, J., Wang, Z., Shi, Z., Zhang, S., Ming, R., Zhu,
S., ... & Chen, N. J. (2013). The genome of the pear (Pyrus
bretschneideri Rehd.). Genome research, 23(2), 396-408. |
|
126. Sork, V. L., Fitz-Gibbon, S. T., Puiu, D., Crepeau, M.,
Gugger, P. F., Sherman, R., ... & Salzberg, S. L. (2016).
First draft assembly and annotation of the genome of a
California endemic oak Quercus lobata Née (Fagaceae). G3:
Genes, Genomes, Genetics, 6(11), 3485-3495. |
|
127. Plomion, C., Aury, J. M., Amselem, J., Leroy, T.,
Murat, F., Duplessis, S., ... & Lesur, I. (2018). Oak genome
reveals facets of long lifespan. Nature plants, 4(7),
440-452. |
|
128. Kitashiba, H. I. R. O. Y. A. S. U., Li, F. E. N. G.,
Hirakawa, H. I. D. E. K. I., Kawanabe, T. A. K. A. H. I. R.
O., Zou, Z. H. O. N. G. W. E. I., Hasegawa, Y. O. I. C. H.
I., ... & Takahata, Y. (2014). Draft sequences of the radish
(Raphanus sativus L.) genome. DNA Research, 21(5), 481-490. |
|
129. Fu, Y., Li, L., Hao, S., Guan, R., Fan, G., Shi, C.,
... & Wang, J. (2017). Draft genome sequence of the Tibetan
medicinal herb Rhodiola crenulata. GigaScience, 6(6),
gix033. |
|
130. Chan, A. P., Crabtree, J., Zhao, Q., Lorenzi, H.,
Orvis, J., Puiu, D., ... & Cahoon, E. B. (2010). Draft
genome sequence of the oilseed species Ricinus communis.
Nature biotechnology, 28(9), 951. |
|
131. Raymond, O., Gouzy, J., Just, J., Badouin, H.,
Verdenaud, M., Lemainque, A., ... & Carrere, S. (2018). The
Rosa genome provides new insights into the domestication of
modern roses. Nature genetics, 50(6), 772-777. |
|
132. Nakamura, N., Hirakawa, H., Sato, S., Otagaki, S.,
Matsumoto, S., Tabata, S., & Tanaka, Y. (2018). Genome
structure of Rosa multiflora, a wild ancestor of cultivated
roses. DNA Research, 25(2), 113-121. |
|
133. Zhang, J., Zhang, X., Tang, H., Zhang, Q., Hua, X., Ma,
X., ... & Wai, C. M. (2018). Allele-defined genome of the
autopolyploid sugarcane Saccharum spontaneum L. Nature
genetics, 50(11), 1565-1573. |
|
134. Garsmeur, O., Droc, G., Antonise, R., Grimwood, J.,
Potier, B., Aitken, K., ... & Costet, L. (2018). A mosaic
monoploid reference sequence for the highly complex genome
of sugarcane. Nature communications, 9(1), 1-10. |
|
135. Salix purpurea v1.0, DOE-JGI,
http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Spurpurea |
|
136. Dai, X., Hu, Q., Cai, Q., Feng, K., Ye, N., Tuskan, G.
A., ... & Luo, W. (2014). The willow genome and divergent
evolution from poplar after the common genome duplication.
Cell research, 24(10), 1274-1277. |
|
137. Banks, J. A., Nishiyama, T., Hasebe, M., Bowman, J. L.,
Gribskov, M., DePamphilis, C., ... & Ashton, N. W. (2011).
The Selaginella genome identifies genetic changes associated
with the evolution of vascular plants. Science, 332(6032),
960-963. |
|
138. Yu, J., Golicz, A. A., Lu, K., Dossa, K., Zhang, Y.,
Chen, J., ... & Zhang, X. (2019). Insight into the evolution
and functional characteristics of the pan-genome assembly
from sesame landraces and modern cultivars. Plant
biotechnology journal, 17(5), 881-892. |
|
139. Bennetzen, J. L., Schmutz, J., Wang, H., Percifield,
R., Hawkins, J., Pontaroli, A. C., ... & Jenkins, J. (2012).
Reference genome sequence of the model plant Setaria. Nature
biotechnology, 30(6), 555. |
|
140. Leisner, C. P., Hamilton, J. P., Crisovan, E.,
Manrique-Carpintero, N. C., Marand, A. P., Newton, L., ... &
Buell, C. R. (2018). Genome sequence of M6, a diploid inbred
clone of the high-glycoalkaloid-producing tuber-bearing
potato species Solanum chacoense, reveals residual
heterozygosity. The Plant Journal, 94(3), 562-570. |
|
141. Tomato Genome Consortium. (2012). The tomato genome
sequence provides insights into fleshy fruit evolution.
Nature, 485(7400), 635. |
|
142. Hirakawa, H., Shirasawa, K., Miyatake, K. O. J. I.,
Nunome, T., Negoro, S., Ohyama, A. K. I. O., ... & Fukuoka,
H. (2014). Draft genome sequence of eggplant (Solanum
melongena L.): the representative solanum species indigenous
to the old world. DNA Research, 21(6), 649-660. |
|
143. Bolger, A., Scossa, F., Bolger, M. E., Lanz, C.,
Maumus, F., Tohge, T., ... & Fich, E. A. (2014). The genome
of the stress-tolerant wild tomato species Solanum
pennellii. Nature genetics, 46(9), 1034-1038. |
|
144. Sharma, S. K., Bolser, D., de Boer, J., Sønderkær, M.,
Amoros, W., Carboni, M. F., ... & Eguiluz, M. (2013).
Construction of reference chromosome-scale pseudomolecules
for potato: integrating the potato genome with genetic and
physical maps. G3: Genes, Genomes, Genetics, 3(11),
2031-2047. |
|
145. McCormick, R. F., Truong, S. K., Sreedasyam, A.,
Jenkins, J., Shu, S., Sims, D., ... & Mattison, A. (2018).
The Sorghum bicolor reference genome: improved assembly,
gene annotations, a transcriptome atlas, and signatures of
genome organization. The Plant Journal, 93(2), 338-354. |
|
146. Xu, C., Jiao, C., Sun, H., Cai, X., Wang, X., Ge, C.,
... & Deng, J. (2017). Draft genome of spinach and
transcriptome diversity of 120 Spinacia accessions. Nature
communications, 8(1), 1-10. |
|
147. Wang, W., Haberer, G., Gundlach, H., Gläßer, C.,
Nussbaumer, T. C. L. M., Luo, M. C., ... & Byrant, D. W.
(2014). The Spirodela polyrhiza genome reveals insights into
its neotenous reduction fast growth and aquatic lifestyle.
Nature communications, 5, 3311. |
|
148. Shoguchi, E., Shinzato, C., Kawashima, T., Gyoja, F.,
Mungpakdee, S., Koyanagi, R., ... & Hamada, M. (2013). Draft
assembly of the Symbiodinium minutum nuclear genome reveals
dinoflagellate gene structure. Current biology, 23(15),
1399-1408. |
|
149. Dassanayake, M., Oh, D. H., Haas, J. S., Hernandez, A.,
Hong, H., Ali, S., ... & Cheeseman, J. M. (2011). The genome
of the extremophile crucifer Thellungiella parvula. Nature
genetics, 43(9), 913. |
|
150. Argout, X., Salse, J., Aury, J. M., Guiltinan, M. J.,
Droc, G., Gouzy, J., ... & Abrouk, M. (2011). The genome of
Theobroma cacao. Nature genetics, 43(2), 101. |
|
151. De Vega, J. J., Ayling, S., Hegarty, M., Kudrna, D.,
Goicoechea, J. L., Ergon, Å., ... & Lang, C. (2015). Red
clover (Trifolium pratense L.) draft genome provides a
platform for trait improvement. Scientific reports, 5,
17394. |
|
152. Hirakawa, H., Kaur, P., Shirasawa, K., Nichols, P.,
Nagano, S., Appels, R., ... & Isobe, S. N. (2016). Draft
genome sequence of subterranean clover, a reference for
genus Trifolium. Scientific reports, 6, 30358. |
|
153. International Wheat Genome Sequencing Consortium.
(2014). A chromosome-based draft sequence of the hexaploid
bread wheat (Triticum aestivum) genome. Science, 345(6194),
1251788. |
|
154. Avni, R., Nave, M., Barad, O., Baruch, K., Twardziok,
S. O., Gundlach, H., ... & Jordan, K. W. (2017). Wild emmer
genome architecture and diversity elucidate wheat evolution
and domestication. Science, 357(6346), 93-97. |
|
155. Ling, H. Q., Ma, B., Shi, X., Liu, H., Dong, L., Sun,
H., ... & Yu, Y. (2018). Genome sequence of the progenitor
of wheat A subgenome Triticum urartu. Nature, 557(7705),
424-428. |
|
156. De Clerck, O., Kao, S. M., Bogaert, K. A., Blomme, J.,
Foflonker, F., Kwantes, M., ... & Califano, G. (2018).
Insights into the evolution of multicellularity from the sea
lettuce genome. Current biology, 28(18), 2921-2933. |
|
157. Ibarra-Laclette, E., Lyons, E., Hernández-Guzmán, G.,
Pérez-Torres, C. A., Carretero-Paulet, L., Chang, T. H., ...
& Fernández-Cortés, A. (2013). Architecture and evolution of
a minute plant genome. Nature, 498(7452), 94-98. |
|
158. Jaillon, O., Aury, J. M., Noel, B., Policriti, A.,
Clepet, C., Casagrande, A., ... & Vezzi, A. (2007). The
grapevine genome sequence suggests ancestral
hexaploidization in major angiosperm phyla. Nature,
449(7161), 463. |
|
159. Prochnik, S. E., Umen, J., Nedelcu, A. M., Hallmann,
A., Miller, S. M., Nishii, I., ... & Hellsten, U. (2010).
Genomic analysis of organismal complexity in the
multicellular green alga Volvox carteri. Science, 329(5988),
223-226. |
|
160. Schnable, P. S., Ware, D., Fulton, R. S., Stein, J. C.,
Wei, F., Pasternak, S., ... & Minx, P. (2009). The B73 maize
genome: complexity, diversity, and dynamics. Science,
326(5956), 1112-1115. |
|
161. Olsen, J. L., Rouzé, P., Verhelst, B., Lin, Y. C.,
Bayer, T., Collen, J., ... & Michel, G. (2016). The genome
of the seagrass Zostera marina reveals angiosperm adaptation
to the sea. Nature, 530(7590), 331-335. |
|
162. Tanaka, H., Hirakawa, H., Kosugi, S., Nakayama, S.,
Ono, A., Watanabe, A., ... & Shimizu, K. (2016). Sequencing
and comparative analyses of the genomes of zoysiagrasses.
DNA Research, 23(2), 171-180. |
|
|
| |
