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1 Supplementary Material Supplementary Table S1. Genomes available in build 47 Supplementary Table S2. Counts of putative contiguous gene split models in 39 plant reference genomes in build 47 Supplementary Table S3. Ontology associations in build 47 Supplementary Table S4. (B)LASTz-chain-net pairwise whole-genome alignments available in build 47 Supplementary Table S5. Synteny analyses in build 47 Supplementary Table S6. Variation data sets housed in the Ensembl variation module in build 47 Supplementary Table S1. Genomes available in build 47 Species Assembly/Gene Space Annotation Variation Aegilops tauschii (goatgrass, wheat D-genome progenitor) Amborella trichopoda Arabidopsis lyrata ASM34733v1/GCA_ GCA_ (AMTR1.0)/ AGD Araly1.0/Araly1.0 Arabidopsis thaliana TAIR10/TAIR10 SNPs & Structural Brachypodium distachyon Brachy1.0/Barchy1.2 SNPs Brassica oleracea Brassica rapa (Chinese cabagge) Chlamydomonas reinhardtii (green algae) Cyanidioschyzon merolae (red algae) Glycine max (soybean) GCA_ /ENA IVFCAASv1/bra_v1.01_SP2010_01 v3.0/ ena ASM9120v1/ ENA Glyma1.0/Glyma1.1 Hordeum vulgare (barley) v2/IBSC_1.0 SNPs Leersia perrieri Medicago truncatula Musa acuminata (banana) GCA_ /OGE MedtrA17_3.5/ EnsemblPlants MA1/ Cirad 1
2 Oryza barthii (complete; Oryza brachyantha (complete; Oryza glaberrima (African rice) Oryza glumaepatula (complete; replaces previous chr. 3s) Oryza longistaminata (complete; replaces previous chr. 3s) Oryza meridionalis (complete; Oryza nivara (complete; Oryza punctata (complete; Oryza rufipogon (complete; Oryza sativa ssp. indica (Asian rice) Oryza sativa ssp. japonica (Asian rice) Ostreococcus lucimarinus Physcomitrella patens (moss) GCA_ /OGE Maker (Aug 2013) [GCA_ ] OGEv1.4b/OGEv1.4 [GCA_ ] AGI1.1 (May 2011)/ AGI (MIPS) GCA_ /OGE Maker (Aug 2013) v aug/oge GCA_ /OGE Maker (Aug 2013) GCA_ /OGE Maker (Aug 2013) GCA_ /OGE Maker (Aug 2013) PRJEB4137/OGE ASM465v1/ BGI IRGSP-1.0/MSU 7.0 v2.0 GCA_ /JGI ASM242v1/ Phypa1.6 SNPs SNPs SNPs Prunus persica (peach) Prupe1_0 / GCA_ /Prupe1_0 / Peach v1.0 Populus trichocarpa (poplar) Selaginella moellendorffii (spikemoss) Setaria italica (foxtail millet) Solanum lycopersicum (tomato) Solanum tuberosum (potato) JGI 2.0/ JGI v1.0/ ena JGIv2.0/JGIv2.1 SL2.50/ITAG2.3 v3.0/soltub_3.0 SNPs 2
3 Sorghum bicolor Sorbi1/ JGI SNPs & Structural Theobroma cacao (cocoa) Triticum aestivum (bread wheat) Triticum urartu (einkorn wheat, A-genome progenitor) GCA_ /ENA IWGSP1/IWGSP1 (MIPS) GCA_ /GCA_ (ENA, Apr 2013) SNPs Vitis vinifera (grape) IGGP 12x/ CRIBI SNPs Zea mays (corn) B73_RefGen_v3/5b+ SNPs Supplementary Table S2. Counts of putative contiguous gene split models (frequently associated with annotation artifacts) in 39 plant reference genomes in build 47 Species Putative contiguous split gene models Aegilops tauschii 740 Amborella trichopoda 994 Arabidopsis lyrata ssp. lyrata 180 Arabidopsis thaliana 37 Brachypodium distachyon 158 Brassica oleracea 911 Brassica rapa ssp. Pekinensis 151 Chlamydomonas reinhardtii 141 Cyanidioschyzon merolae 8 Glycine max 390 Hordeum vulgare ssp. Vulgare 108 Leersia perrieri 189 Medicago truncatula 394 Musa acuminata 1624 Oryza barthii 338 3
4 Oryza brachyantha 302 Oryza glaberrima 518 Oryza glumaepatula 394 Oryza longistaminata 291 Oryza meridionalis 272 Oryza nivara 310 Oryza punctata 282 Oryza rufipogon 300 Oryza sativa ssp. indica 796 Oryza sativa ssp. japonica 636 Ostreococcus lucimarinus 26 Physcomitrella patens subsp. Patens 276 Populus trichocarpa 1651 Prunus persica 448 Selaginella moellendorffii 215 Setaria italica 332 Solanum lycopersicum 1216 Solanum tuberosum 653 Sorghum bicolor 953 Theobroma cacao 113 Triticum aestivum 1234 Triticum urartu 674 Vitis vinifera 725 Zea mays 844 4
5 Supplementary Table S3. Ontology associations in build 47 Prefix Species Total Count GO Aegilops tauschii 4233 Arabidopsis lyrata 5397 Arabidopsis thaliana 5463 Brachypodium distachyon 4483 Brassica rapa 4712 Chlamydomonas reinhardtii 3666 Cyanidioschyzon merolae 2169 Glycine max 4779 Hordeum vulgare 4714 Medicago truncatula 4580 Musa acuminata 4511 Oryza brachyantha 4837 Oryza glaberrima 4745 Oryza sativa ssp. indica 5171 Oryza sativa ssp. japonica 5115 Physcomitrella patens 4218 Populus trichocarpa
6 Selaginella moellendorffii 4267 Setaria italica 4852 Solanum lycopersicum 4804 Solanum tuberosum 4568 Sorghum bicolor 5000 Triticum aestivum 4388 Triticum urartu 4257 Vitis vinifera 5116 Zea mays 4681 PO Arabidopsis thaliana 594 Brachypodium distachyon 3 Physcomitrella patens 4 Solanum lycopersicum 75 Vitis vinifera 23 Zea mays 56 Supplementary Table S4. (B)LASTz-chain-net pairwise whole-genome alignments available in build 47 6
7 Supplementary Table S5. Synteny analyses in build 47 7
8 Supplementary Table S6. Variation data sets housed in the Ensembl variation module in build 47 Species Variants Source Studies Arabidopsis thaliana 14,234, K SNPs x 1179 accessions SV: 13, genomes project: 411 resequenced accessions (Clark et al, 2007, Atwell et al, 2010, Gan et al, 2011) Brachypodium distachyon 327,988 3 accessions of Brachypodium sylvaticum (Fox et al, 2013) Hordeum vulgare 19,474,539 Resequencing 4 accessions plus wild barely & RNA-Seq (Illumina HiSeq 2000) from embryos of 9 cultivars and Morex ~5M from 90 Morex x Barke (International Barley Genome Sequencing et al, 2012) (Fox et al, 2014) ~6M from 84 8
9 Oregon Wolfe Oryza glaberrima 7,172,036 Resequenced 20 accessions African rice & wild progenitor O. barthii Oryza Genome Evolution project Oryza sativa ssp. japonica Oryza sativa ssp. indica Solanum lycopersicum 5,512, K SNPs x 20 accessions 1311 SNPs x 395 accessions ~4M BGI Japonica vs Indica SNPs 5,418,373 ~4M BGI Japonica vs Indica SNPs 71,156,450 WGS of 84 tomato accessions & related species (McNally et al, 2009) (Zhao et al, 2010) NCBI dbsnp NCBI dbsnp (Tomato Genome Sequencing et al, 2014) Sorghum bicolor SV: 32,246 Genomic Variants archive (dgva) (Zheng et al, 2011) 265,000 SAP, MCC, RS (Morris et al, 2013) 6,578,420 (Mace et al, 2013) Triticum aestivum 12,220,924 ~1.57 M SNPs from the Wheat HapMap. ~725,000 nonredundant SNP from CerealsDB (Axiom, iselect and KASP array sets) & ~10.3M interhomoeologous variants may be visualized or retrieved through the genome browser Vitis vinifera 457,404 Resequencing USDA germplasm collection (Jordan et al, 2015); CerealsDB (Myles et al, 2010) Zea mays 51,162,745 HapMap1: NAM (Gore et al, 2009) 9
10 founder lines HapMap2: predomesticated & domesticated lines Panzea 2.7 GBS (Chia et al, 2012) Panzea.org Supplementary References Atwell, S., et al. (2010). "Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines." Nature 465(7298): Chia, J. M., et al. (2012). "Maize HapMap2 identifies extant variation from a genome in flux." Nat Genet 44(7): Clark, R. M., et al. (2007). "Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana." Science 317(5836): Fox, S. E., et al. (2014). "De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum." PLoS One 9(5): e Fox, S. E., J. Preece, J. A. Kimbrel, G. L. Marchini, A. Sage, K. Youens-Clark, M. B. Cruzan and P. Jaiswal (2013). "Sequencing and De Novo Transcriptome Assembly of Brachypodium sylvaticum (Poaceae).." Applications in Plant Sciences 1(3): Gan, X., et al. (2011). "Multiple reference genomes and transcriptomes for Arabidopsis thaliana." Nature 477(7365): Gore, M. A., et al. (2009). "A first-generation haplotype map of maize." Science 326(5956):
11 International Barley Genome Sequencing, C., et al. (2012). "A physical, genetic and functional sequence assembly of the barley genome." Nature 491(7426): Jordan, K. W., et al. (2015). "A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes." Genome Biol 16: 48. Mace, E. S., et al. (2013). "Whole-genome sequencing reveals untapped genetic potential in Africa's indigenous cereal crop sorghum." Nat Commun 4: McNally, K. L., et al. (2009). "Genomewide SNP variation reveals relationships among landraces and modern varieties of rice." Proc Natl Acad Sci U S A 106(30): Morris, G. P., et al. (2013). "Population genomic and genome-wide association studies of agroclimatic traits in sorghum." Proc Natl Acad Sci U S A 110(2): Myles, S., J. M. Chia, B. Hurwitz, C. Simon, G. Y. Zhong, E. Buckler and D. Ware (2010). "Rapid genomic characterization of the genus vitis." PLoS One 5(1): e8219. Tomato Genome Sequencing, C., et al. (2014). "Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing." Plant J 80(1): Zhao, K., et al. (2010). "Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome." PLoS One 5(5): e Zheng, L. Y., et al. (2011). "Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor)." Genome Biol 12(11): R
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