Sequenced plant genomes

This site attempts to track all plant genomes with published sequences, and at least some of the genomes currently in the process of being sequenced

Eudicots

The eudicots are the largest group of flowering plants on the planet.

Asterids

The asterids are a group of plants within the eudicots that include species like the solanacious vegetables (Tobacco, Tomato, Potato, and Eggplant) and the sunflowers.

• Tomato: The tomato genome project is not yet complete. The version of the genome currently loaded into CoGe is assembled into pseudomolecules but does not contain . Read more about the tomato genome here (add link to their page) or see it in GenomeView here.

• Potato: The potato genome project is not yet complete. Read more about the potato genome here (add link to their page) or see it in GenomeView here.

• Monkey Flower: The monkey flower/mimulus genome is not yet complete. The version of the genome currently loaded into CoGe is not assembled into pseudomolecules but does contain genome models Read more about the monkey flower genome here (add link to their page) or see it in GenomeView here.

Rosids

Grape

The genome sequence of the european grape (Vitis vinifera) was published by a group of French and Italian researchers in 2007. The variety of grape sequenced was the Pinot Noir.

Grape diverged early from the two main groups of species in the rosids (eurosids I and eurosids II) and has not experienced any whole genome duplications since that divergence making it an important outgroup for comparisons to other rosid species as well as providing a great resource for studying the ancient hexaploidy that preceeding the radiation of rosid species (and possibly the radiation of eudicot species).

The version of the grape genome in CoGe contains ~500 megabases of sequence and X annotated genes spread across 19 chromosomes.

The genome paper:

Jaillon, O., Aury, J., Noel, B., Policriti, A., Clepet, C., Casagrande, A., Choisne, N., Aubourg, S., Vitulo, N., Jubin, C., Vezzi, A., Legeai, F., Hugueney, P., Dasilva, C., Horner, D., Mica, E., Jublot, D., Poulain, J., Bruyère, C., Billault, A., Segurens, B., Gouyvenoux, M., Ugarte, E., Cattonaro, F., Anthouard, V., Vico, V., Del Fabbro, C., Alaux, M., Di Gaspero, G., Dumas, V., Felice, N., Paillard, S., Juman, I., Moroldo, M., Scalabrin, S., Canaguier, A., Le Clainche, I., Malacrida, G., Durand, E., Pesole, G., Laucou, V., Chatelet, P., Merdinoglu, D., Delledonne, M., Pezzotti, M., Lecharny, A., Scarpelli, C., Artiguenave, F., Pè, M., Valle, G., Morgante, M., Caboche, M., Adam-Blondon, A., Weissenbach, J., Quétier, F., & Wincker, P. (2007). The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla Nature, 449 (7161), 463-467 DOI: 10.1038/nature06148

Eurosids 1

Cucumber

The genome sequence of cucumber (Cucumis sativus) was published in late 2009. The genome was sequenced using a combination of Illumina short read sequencing (68.3x coverage) and Sanger sequencing (3.9x coverage). The cucumber genome is made up of seven chromosomes, but a large fraction of the published genome sequence is still in unordered contigs. The version of the cucumber genome in CoGe contains ~200 megabases of DNA sequence and X gene models spread over 4219 contigs.

The genome paper: Huang, S., Li, R., Zhang, Z., Li, L., Gu, X., Fan, W., Lucas, W., Wang, X., Xie, B., Ni, P., Ren, Y., Zhu, H., Li, J., Lin, K., Jin, W., Fei, Z., Li, G., Staub, J., Kilian, A., van der Vossen, E., Wu, Y., Guo, J., He, J., Jia, Z., Ren, Y., Tian, G., Lu, Y., Ruan, J., Qian, W., Wang, M., Huang, Q., Li, B., Xuan, Z., Cao, J., Asan, ., Wu, Z., Zhang, J., Cai, Q., Bai, Y., Zhao, B., Han, Y., Li, Y., Li, X., Wang, S., Shi, Q., Liu, S., Cho, W., Kim, J., Xu, Y., Heller-Uszynska, K., Miao, H., Cheng, Z., Zhang, S., Wu, J., Yang, Y., Kang, H., Li, M., Liang, H., Ren, X., Shi, Z., Wen, M., Jian, M., Yang, H., Zhang, G., Yang, Z., Chen, R., Liu, S., Li, J., Ma, L., Liu, H., Zhou, Y., Zhao, J., Fang, X., Li, G., Fang, L., Li, Y., Liu, D., Zheng, H., Zhang, Y., Qin, N., Li, Z., Yang, G., Yang, S., Bolund, L., Kristiansen, K., Zheng, H., Li, S., Zhang, X., Yang, H., Wang, J., Sun, R., Zhang, B., Jiang, S., Wang, J., Du, Y., & Li, S. (2009). The genome of the cucumber, Cucumis sativus L. Nature Genetics, 41(12), 1275-1281 DOI: 10.1038/ng.475

Poplar

The genome sequence of the black cottonwood tree (Populus trichocarpa) was published in 2006. The genome was originally sequenced to a coverage of 7.5x using Sanger sequencing. Poplar was the third plant genome to be published, and is now one of two published genomes of tree species (the other being papaya). Poplar contains a whole genome duplication that is not shared by any other plant species with a sequenced genome. The most recent version of the poplar genome in CoGe is v2 available on Phytozome which includes ~370 megabases of sequence and 41377 protein coding genes spread over 19 chromosomes.

The genome paper: Tuskan, G., DiFazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., Hellsten, U., Putnam, N., Ralph, S., Rombauts, S., Salamov, A., Schein, J., Sterck, L., Aerts, A., Bhalerao, R., Bhalerao, R., Blaudez, D., Boerjan, W., Brun, A., Brunner, A., Busov, V., Campbell, M., Carlson, J., Chalot, M., Chapman, J., Chen, G., Cooper, D., Coutinho, P., Couturier, J., Covert, S., Cronk, Q., Cunningham, R., Davis, J., Degroeve, S., Dejardin, A., dePamphilis, C., Detter, J., Dirks, B., Dubchak, I., Duplessis, S., Ehlting, J., Ellis, B., Gendler, K., Goodstein, D., Gribskov, M., Grimwood, J., Groover, A., Gunter, L., Hamberger, B., Heinze, B., Helariutta, Y., Henrissat, B., Holligan, D., Holt, R., Huang, W., Islam-Faridi, N., Jones, S., Jones-Rhoades, M., Jorgensen, R., Joshi, C., Kangasjarvi, J., Karlsson, J., Kelleher, C., Kirkpatrick, R., Kirst, M., Kohler, A., Kalluri, U., Larimer, F., Leebens-Mack, J., Leple, J., Locascio, P., Lou, Y., Lucas, S., Martin, F., Montanini, B., Napoli, C., Nelson, D., Nelson, C., Nieminen, K., Nilsson, O., Pereda, V., Peter, G., Philippe, R., Pilate, G., Poliakov, A., Razumovskaya, J., Richardson, P., Rinaldi, C., Ritland, K., Rouze, P., Ryaboy, D., Schmutz, J., Schrader, J., Segerman, B., Shin, H., Siddiqui, A., Sterky, F., Terry, A., Tsai, C., Uberbacher, E., Unneberg, P., Vahala, J., Wall, K., Wessler, S., Yang, G., Yin, T., Douglas, C., Marra, M., Sandberg, G., Van de Peer, Y., & Rokhsar, D. (2006). The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray) Science, 313 (5793), 1596-1604 DOI: 10.1126/science.1128691

Legumes

Legumes (the plant family Fabaceae) contained within the eurosid II clade. The family is perhaps best known for the fact that many of the species it contains form symbiotic relationships with nitrogen fixing bacteria. The bacteria are sheltered and feed within special nodules in the roots of these plants and in return the plant benefits from the bacteria's ability to convert the nitrogen in our atmosphere into bio-available forms (bioavailable nitrogen is often a limiting nutrient for other plant species).

Eurosids 2

Papaya

The genome of the papaya tree (Carica papaya) was published in the early 2008. Papaya was one of the earliest crops to be genetically modified (in papaya's case to resist the devastating papaya ringspot virus) and the sequenced genome actually comes from one of the genetically modified varieties (SunUp). The papaya genome was sequenced to a coverage of 3x using Sanger sequencing. Papaya has not experienced further [whole genome duplications] since the ancient hexaploidy shared by all currently sequenced eudicots. As the most closely related species to Arabidopsis with a currently sequenced genome that has not experienced the two subsequence whole genome duplications found in the Arabidopsis lineage, papaya is a useful outgroup, although the ancestors of Arabidopsis and Papaya split ~72 million years ago.

The papaya genome is estimated to be have a size of 372 megabases, spread across nine chromosomes, and contain (X) genes. The version of papaya within CoGe is organized into super contigs, but does contain a number of gaps.

The genome paper:

Ming, R., Hou, S., Feng, Y., Yu, Q., Dionne-Laporte, A., Saw, J., Senin, P., Wang, W., Ly, B., Lewis, K., Salzberg, S., Feng, L., Jones, M., Skelton, R., Murray, J., Chen, C., Qian, W., Shen, J., Du, P., Eustice, M., Tong, E., Tang, H., Lyons, E., Paull, R., Michael, T., Wall, K., Rice, D., Albert, H., Wang, M., Zhu, Y., Schatz, M., Nagarajan, N., Acob, R., Guan, P., Blas, A., Wai, C., Ackerman, C., Ren, Y., Liu, C., Wang, J., Wang, J., Na, J., Shakirov, E., Haas, B., Thimmapuram, J., Nelson, D., Wang, X., Bowers, J., Gschwend, A., Delcher, A., Singh, R., Suzuki, J., Tripathi, S., Neupane, K., Wei, H., Irikura, B., Paidi, M., Jiang, N., Zhang, W., Presting, G., Windsor, A., Navajas-Pérez, R., Torres, M., Feltus, F., Porter, B., Li, Y., Burroughs, A., Luo, M., Liu, L., Christopher, D., Mount, S., Moore, P., Sugimura, T., Jiang, J., Schuler, M., Friedman, V., Mitchell-Olds, T., Shippen, D., dePamphilis, C., Palmer, J., Freeling, M., Paterson, A., Gonsalves, D., Wang, L., & Alam, M. (2008). The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus) Nature, 452 (7190), 991-996 DOI: 10.1038/nature06856

Arabidopsis

Arabidopsis thaliana is a poplar model plant species, partially as a result of its short generation time and compact size. The genome of Arabidopsis was also the first plant genome to be published back in 2000. The current release of the Arabidopsis genome is TAIR9:

The TAIR9 release contains 27,379 protein coding genes, 4827 pseudogenes or 
transposable elements and 1312 ncRNAs (33,518 genes in all, 39,640 gene models). 

The Arabidopsis genome is ~120 megabases of sequence spread across five chromosomes.

Genome resources:

The TAIR homepage

Arabidopsis lyrata genome:

Arabidopsis lyrata also has a sequenced, though unpublished, genome. As a close relative of A. thaliana, the lyrata genome is valuable for comparative genomics. A. lyrata also is self-incompatable, while A. thaliana reproduced primarily through self-fertilization. The lyrata genome is available within CoGe.

The 1001 genomes project plans to sequence the genomes of 1001 different varieties of Arabidopsis. Currently 88 are available with more in progress.

The Genome Paper: The Arabidopsis Genome Initiative (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408 (6814), 796-815 DOI: 10.1038/35048692

Monocots

• Banana