Supplementary Figure 1. The tree of Chinese jujube and its growing environment. The jujube has a very long lifecycle, even more than 1000 productive

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1 Supplementary Figure 1. The tree of Chinese jujube and its growing environment. The jujube has a very long lifecycle, even more than 1000 productive years. It is well adapted to drought and salinity.

2 Supplementary Figure2. 17-mer frequency distribution of sequencing reads and heterozygosity simulation. A K-mer refers to an artificial sequence division of K nucleotides. A sequencing read with L bp contains (L-K+1) K-mers if the length of each K-mer is K bp. Typically, K was set as 17 for genome size estimation. The K-mer frequency follows a Poisson distribution in a given data set. During deduction, the genome size G=K_num/Peak_depth, where the K_num is the total number of K-mer, and Peak_depth is the expected value of K-mer depth. Furthermore, if the heterozygous rate is higher, then a small peak will be presented at 1/2 of Peak_depth. So this K-mer analysis can be used to roughly determine the heterozygous rate of a given genome. The x-axis is depth (X); the y-axis is the proportion, which represents the frequency at that depth divide by the total frequency of all the depth. The high heterozygosis rate of jujube caused a sub peak (depth 30X) at the position of the half of the main peak (depth 59X). M is stand for heterozygosity, and the two curves are derived from heterozygosis simulation. The heterozygosis simulation revealed that the heterozygosis ratio was about 1.9% (between 1.8% and 2.0%).

3 2 Ziziphus jujuba 405 Mb, avg_gc: Vitis vinifera 486 Mb, avg_gc: Prunus persica 227 Mb, avg_gc: percent of bins, bin=500 bp G+C Content Supplementary Figure 3. GC distribution in Ziziphus jujuba, Vitis vinifera and Prunus persica.

Supplementary Figure 4. The pseudo-molecules of the 12 chromosomes ordered by genetic length. Construction of the genetic map with 55,743 segregated SNP sites, we got all the genotype s X 2 test.

4 Supplementary Figure 4. The pseudo-molecules of the 12 chromosomes ordered by genetic length. Construction of the genetic map with 55,743 segregated SNP sites, we got all the genotype s X 2 test. In Join map 4.0, X 2 10 (P value 0.01). At last, we just have 4033 SNP remained. With these markers, the genetic map had been constructed. The parameter was LOD start-end (7.0 to 15, step, 1.0). The locations of the 4 randomly selected BACs analyzed in Supplementary Fig. 5 are shown by red arrows.

of the jujube assembly, read depth on the

5 Supplementary Figure 5. Alignments for the 4 randomly picked BAC clones and scaffolds. To evaluate the completeness and accuracy of the jujube assembly, read depth on the BACs was calculated by mapping the short reads onto the BAC sequences. The predicted genes, SSR and annotated transposable elements (TEs) are shown, respectively.

6 Supplementary Figure 6. The tissue-specific genes of the jujube.

7 Supplementary Figure 7. Divergence rate of transposable elements in the jujube genome. The divergence rate was calculated based on the alignment between the RepeatMasker annotated repeat copies and the consensus sequence in the repeat library (RepBase).

8 Supplementary Figure 8. The synteny of some gene blocks in Chr1 ( Mb) with other chromosomes.

9 a b c d Supplementary Figure 9. Deciduous bearing shoot (D) and persistently lignified bearing shoot (P). a, fruiting status of D; b, fruiting status of P; c, left shows the joint point of D and right shows the joint point of P; d, the stem of D (lower) and P (up) after removing leaves.

10 Supplementary Table 1 The wide adaptation of Chinese jujube Parameter Value Minimum annual average temperature ( C) 5.5 Maximum annual average temperature ( C) 22 The lowest temperature ( C) Minimum frost-free period (days) 100 Annual rainfall (mm) Minimum annual sunshine (hr) 1100 ph Maximum soil water NaCl concentration (%) 0.15 Maximum soil water Na 2 CO 3 concentration (%) 0.3 Supplementary Table 2 Jujube nutritional facts in comparison to other (fruit) crops Fruit species Carbohydrate (%) Vc (mg/100g) Mineral element (mg/100g) Ca K Fe Zn Jujube Apple Peach Persimmon Grape Orange Pineapple Litchi Chestnut Walnut Sugarcane Sugar beet Kiwifruit Date from China Food Composition (2009) 1. means no data. Supplementary Table 3 Estimation of jujube genome size based on K-mer statistics K-mer K-mer number K-mer depth Genome Size Used Base Used Read Coverage 17 26,191,979, ,931,860 31,430,375, ,399, From the distribution curve of depth-frequency (Supplementary Fig.2), we get that the expected depth is 59 and the total input reads number is 327,399,747, the total base is 31,430,375,712, the total K-mer number is 26,191,979,760. We calculated the genome size according to the formula: Genome Size =K-mer_num/Peak_depth 2.

11 Supplementary Table 4 Comparison of jujube genome features with those of other 9 species Species Jujube (Ziziphus jujuba) Mulberry (Morus alba) Kiwifruit (Actinidia chinensis) Peach (Prunus persica) Pear (Pyrus bretschneideri) Apple (Malus domestica) Strawberry (Fragaria vesca) Poplar (Populus trichocarpa) Sweet orange (Citrus sinensis) Family Genome size (Mb) Heterozygosity (%) Repeat elements (%) Rhamnaceae Moraceae Arctinaceae Rosaceae Rosaceae Rosaceae Rosaceae Salicaceae Rutaceae Prunus mume Rosaceae Data from our research and the papers on the genome of relevant species, and means no data. GC content (%)

12 Supplementary Table 5 SSR distribution of jujube and six closely-related species Species Jujube Apple 3 Pear 4 Peach 5 Strawberry 6 Prunus mume 7 Mulberry 8 Total size of examined sequences (Mb) Distribution of different repeat classes Number of di-nucleotide repeats 106,537 84,914 50,455 32,038 23,054 33,763 58,651 Number of tri-nucleotide repeats 38,168 25,955 11,829 8,086 7,910 8,698 20,072 Number of tetra-nucleotide repeats 7,144 3,718 3,314 1, ,668 3,515 Number of penta-nucleotide repeats Number of hexa-nucleotide repeats Total 153, ,870 66,449 42,367 32,102 44,719 83,544 SSR density ( /Mb) Data from our research and the papers on the genome of relevant species. We found SSR sequence for jujube genome using SSRIT ( Supplementary Table 6 SSR comparison of jujube and grape or peach in collinear gene blocks (gene pairs 20) Jujube vs Grape Jujube vs Peach Jujube Grape Jujube/Grape Jujube Peach Jujube/Peach Number of blocks Gene pairs 2,911 4,391 Block length (N counted in bp) 44,869,077 91,407,764 74,625,771 81,675,856 Block length (without N, bp) 46,671,967 93,327,470 77,585,925 82,140,745 GC content (%) Number of SSR 7,963 6,286 13,031 8,023 Total length of SSR (bp) 230, , , ,967 Percent of SSR (%) We found SSR sequence for the three genomes using SSRIT (

13 Supplementary Table 7 Construction of libraries and the generation and filtering of the sequencing data used for the genome assembly Raw data Clean data Insert size Read length(bp) Total data(gb) Sequence coverage(x) Physical coverage(x) Read length(bp) Total data(gb) Sequence coverage(x) Physical coverage(x) 170bp bp bp bp kb kb kb kb kb Total We construct different insert-size WGS libraries using DNA sample of jujube. According to the strategy, the insert size of library is: 170bp, 250bp, 500bp, 800bp, 2Kb, 5Kb, 10Kb, 20Kb and 40Kb. After library constructing, we use Hiseq2000 to sequence PE reads for each library. Assuming the genome size is 444Mb. The quality requirement for de novo sequencing is far higher than re-sequencing. In order to facilitate the assembling works, we have taken a series of checking and filtering measures on raw data (generated by Solexa-Pipeline) to get clean data. We filtered raw reads to generate clean reads by the following criteria: (1) we remove reads with >2% Ns or with poly-a structure; (2) we remove reads with 40% low quality bases for short insert size libraries, and 60% for large insert size libraries; (3) we remove reads containing adapters; (4) we remove paired reads with mutual overlaps; (5) we remove PCR duplicates. After filtering, Gb high-quality data were retained, which representing genome coverage.

14 Supplementary Table 8 BAC data statistics Insert Size Number of libraries Number of lanes Total Raw Data (G) Total Clean Data (G) 500bp 21, Total 21, ,504 BAC clones with 120 kb in average length were randomly selected (about 5.8 genome size of jujube) and one 500bp WGS library was constructed for each clone. All libraries were sequenced on the Illumina HiSeq 2000 sequencing system. Supplementary Table 9 Statistics of the final genome assembly Contig Scaffold Size (bp) Number Size(bp) Number N90 7,347 13,344 73,568 1,497 N80 13,410 9, ,418 1,066 N70 19,527 6, , N60 26,037 4, , N50 33,948 3, , Longest 334, ,141, Total size 417,332, ,645, Total Number( 100bp) , ,898 Total Number( 2kb) , ,139 Supplementary Table 10 Assessment of genome coverage for four randomly selected BAC clones Number of Number of Aligned BAC Length Coverage Number alignment aligned scaffold length ID (bp) ratio (%) of gaps blocks scaffolds (bp) Gap length (bp) Gap ratio (%) BAC1 107, , BAC2 112, ,035, , BAC3 128, ,723, , BAC4 106, , The jujube assembly (scaffolds) was then aligned to four Sanger-sequenced BACs (average length kb) via BLASTN. The coverage of the BAC sequences by our assembled scaffolds was calculated. Supplementary Table 11 Assessment of the transcript coverage with data from the 1942 published ESTs Bases Sequences with > 90% sequence with > 50% sequence Dataset Number Total length (bp) covered by covered by in one scaffold in one scaffold assembly assembly Number Percent Number Percent > 0 bp 1,942 1,169, , , > 200 bp 1,933 1,167, , , > 500 bp 1, , , , Data from downloaded on July, 2013 Supplementary Table 12 Assessment of the transcript coverage with the transcriptome assembly contig (TAC) data Dataset Number Total length (bp) Bases covered by assembly Sequences Covered by assembly with > 90% sequence in one scaffold with > 50% sequence in one scaffold Number Percent Number Percent > 0 bp 51,514 46,167, , , > 200 bp 51,514 46,167, , , > 500 bp 26,805 38,578, , , > 1000 bp 16,059 30,851, , ,

15 Supplementary Table 13 The alignment results of two parents and their 105 progenies Sample ID Paired mapping(pe) (PE%) Singled mapping(se) Mapping Reads (SE%) All mapping (All mapping%) P1 6,655, ,383, ,038, P2 4,272, , ,220, S100 5,787, ,258, ,046, S101 7,002, ,833, ,835, S102 3,031, , ,718, S103 3,778, , ,773, S104 4,637, ,247, ,884, S105 3,796, ,019, ,816, S106 4,244, ,049, ,293, S107 4,348, ,305, ,653, S108 3,215, , ,935, S109 5,374, ,439, ,813, S10 10,434, ,260, ,694, S110 5,844, ,559, ,403, S111 3,756, ,113, ,869, S112 3,962, ,072, ,035, S113 4,091, , ,041, S114 3,961, ,099, ,061, S115 4,849, ,179, ,029, S116 5,235, ,365, ,601, S117 5,622, ,551, ,173, S118 4,470, ,233, ,703, S119 4,232, ,148, ,380, S12 2,423, , ,853, S13 7,729, ,464, ,194, S14 3,398, , ,996, S15 2,799, , ,287, S16 3,598, , ,327, S17 4,521, , ,330, S18 3,611, , ,287, S19 17,532, ,639, ,171, S20 8,059, ,599, ,659, S21 7,130, ,398, ,528, S22 1,557, , ,815, S24 4,729, , ,655, S25 6,815, ,355, ,170, S27 9,072, ,913, ,986, S28 2,887, , ,417, S2 7,815, ,604, ,419, S31 4,360, , ,163, S32 4,000, , ,778, S33 2,404, , ,841, S36 4,771, , ,724, S37 1,835, , ,176, S38 11,287, ,389, ,677, S39 3,069, , ,655, S3 2,460, , ,937, S40 7,756, ,520, ,277, S41 12,025, ,325, ,350, S42 5,401, ,027, ,429, S43 3,094, , ,685, S44 5,473, ,096, ,569, S45 2,952, , ,499, S46 5,005, ,088, ,093, S47 12,866, ,630, ,497, S49 3,467, , ,135, S50 5,366, ,060, ,426, S52 4,576, , ,507, S53 3,779, , ,432, S54 7,630, ,361, ,991, S55 12,735, ,375, ,110, S56 5,653, ,438, ,091,

16 S57 4,833, ,127, ,960, S58 6,391, ,649, ,040, S59 6,043, ,516, ,560, S62 4,951, ,269, ,220, S63 5,584, ,477, ,061, S64 5,839, ,582, ,422, S65 4,329, ,058, ,387, S66 5,436, ,396, ,833, S67 6,241, ,613, ,854, S68 3,499, , ,393, S69 4,754, ,222, ,976, S6 12,991, ,596, ,588, S70 9,145, ,980, ,125, S71 4,969, , ,933, S72 7,649, ,872, ,521, S73 7,718, ,924, ,643, S74 5,927, ,551, ,479, S75 4,449, ,281, ,731, S76 4,335, ,192, ,528, S77 4,064, ,147, ,211, S78 4,642, ,249, ,891, S79 4,452, ,183, ,636, S7 5,772, ,123, ,896, S80 4,578, ,127, ,706, S81 5,425, ,559, ,985, S82 4,890, ,306, ,197, S83 5,403, ,475, ,878, S84 4,470, ,035, ,505, S85 3,051, , ,707, S86 5,840, ,491, ,331, S87 2,365, , ,846, S88 3,087, , ,796, S89 4,329, ,167, ,497, S8 7,591, ,395, ,987, S90 5,211, ,325, ,536, S91 4,212, ,148, ,360, S92 3,341, , ,251, S93 5,545, ,487, ,033, S94 2,605, , ,347, S95 5,225, ,469, ,695, S96 5,541, ,361, ,903, S97 4,292, ,037, ,330, S98 6,647, ,776, ,424, S99 6,146, ,680, ,827, S9 15,026, ,632, ,659, Supplementary Table 14 General statistics of predicted protein-coding genes for jujube Annotation methods Number Average transcript length (bp) Average CDS length (bp) Average exon per gene Average exon length (bp) Average intron length (bp) De novo AUGUSTUS 41,367 3, , Genescan 40,451 6, , , C. sinensis 22,510 3, , M. domestica 22,400 3, , Homolog P. trichocarpa 22,989 3, , G. max 21,523 3, , P. persica 23,322 2, , V. vinifera 20,926 3, , GLEAN 28,585 4, , RNASeq 29,051 4, , , Final gene 32,808 3, ,

17 Supplementary Table 15 Functional annotation of predicted genes for jujube Number Percentage (%) Total 32, Annotated InterPro 3, GO 3, KEGG 15, SwissProt 21, TrEMBL 26, Unannotated 5, Supplementary Table 16 The numbers of genes with certain numbers of exons in the jujube genome Total gene number 32,808 Number of genes containing one exon 7,128 (21.73%) Number of genes containing two exons 5,195 (15.83%) Number of genes containing three exons 5,579 (17.00%) Number of genes containing more than three exons 14,906 (45.43%) Supplementary Table 17 The numbers of genes with certain numbers of exons in the jujube genome Total length of annotation genes(nt) Covered by transcript reads from different tissue(nt) Coverage rate(%) Supplementary Table 18 Identification of non-coding RNA genes in the jujube genome Type Copy Average length (bp) Total length (bp) % of genome mirna , trna 1, , Total rrna , S , rrna 28S , S , S , Total snrna , CD-box , snrna HACA-box , Splicing , CD-box: C box (UGAUGA) and the D box (CUGA); HACA-box: H/ACA-type snornas Supplementary Table 19 General statistics of SNPs in the jujube genome SNP number Effective length (bp) SNP density (/kb) Chromosome level 3,794, ,005, Scaffold level 4,769, ,332, Rate of anchored (%) Supplementary Table 20 General statistics of jujube repetitive elements Type Repeat Size (bp) Rate of Genome (%) TRF 23,048, RepeatMasker 47,307, RepeatProteinMask 52,059, De novo 199,215, Total 216,570,

18 Supplementary Table 21 Classification of jujube transposable elements Retrotransposons Types Length (bp) Rate of Transposable Elements (%) Rate of Genome (%) Total of Retrotransposons 166,416, Gypsy 75,815, Copia 55,318, Line 7,741, Sine 856, Other 6, Unclassified elements 26,679, DNA transposons 38,501, Total transposable elements 204,918, Supplementary Table 22 Summary of synteny blocks among Z. jujuba, F. vesca, V. vinifera and P. persica Genome Block size Total < 1Mb 1-3Mb > 3M Ziziphus jujuba vs Fragaria vesca Fragaria vesca vs Ziziphus jujuba Ziziphus jujuba vs Vitis vinifera Vitis vinifera vs Ziziphus jujuba Ziziphus jujuba vs Prunus persica Prunus persica vs Ziziphus jujuba Supplementary Table 23 Fructose, glucose, sucrose and total sugar content in different stages of fruit (mg/g DW) Stage Sucrose Glucose Fructose Total sugar Young fruit White mature fruit Half red fruit Full red fruit Supplementary Table 24 The log2 ratio of expression values (RPKM) of genes related to plant hormone signal transduction in deciduous and lignified bearing shoots of jujube Gene ID Log2 ratio Up/Down Predicted Deciduous Lignified (lignified/ Regulation(lignified/ Gene deciduous) deciduous) P-value FDR CCG SAUR Up E-07 CCG SAUR Up E-07 CCG SAUR Up E-35 CCG CYCD Up E-93 CCG CYCD Up E-129 CCG ARR-A Up E-68 addgene1990 ARR-A Up E-46 CCG PYL Down E-05 CCG PYL Down E-08 CCG SNRK Down E-05 CCG ERF Down E-22 CCG ERF Down E-16 CCG JAR Down E-21 P-value corresponds to differential gene expression test. Since gene expression analysis generates a large multiplicity problems in which thousands of hypothesis (is gene x differentially expressed between the two groups) are tested simultaneously, correction for false positive (type I errors) and false negative (type II) errors are performed. Assume that we have picked out R differentially expressed genes in which S genes really show differential expression and the other V genes are false positive. If we decide that the error ratio Q = V / R must stay below a cutoff (e.g. 5%), we should preset the FDR to a number no larger than We use FDR and the absolute value of Log2 Ratio 1 as the threshold to judge the significance of gene expression difference.

19 Supplementary Table 25 The expression of genes involved in the response to osmotic stress at different stages of fruit (RPKM) Gene Young fruit White mature fruit Half red fruit Full red fruit CCG CCG CCG addgene CCG CCG Supplementary Table 26 The high expression of chitinase genes in jujube (RPKM) Gene Primary shoot Secondary shoot Bearing shoot Mother shoot CCG CCG CCG CCG CCG CCG CCG KEGG_Orthology K e gmx: c hitinase [EC: ] K e zma: c hitinase [EC: ] K e rcu:rcom_ chitinase [EC: ] K e osa: chiti nase [EC: ] K e gmx: c hitinase [EC: ] K e vvi: ch itinase [EC: ] K e pop:poptr_ chitinase [EC: ] The gene expression level is calculated by using RPKM 9 method (Reads per kilobase transcriptome per million mapped reads). Supplementary Table 27 The number of genes encoding autophagy-related protein 9 in jujube and other species IPR_ID Z. jujuba F. vesca M. alba M.domestica P. bretschneider P. mume P. persica p_value IPR IPR ID reference to the InterPro database Supplementary Table 28 R genes in jujube and 11 other species Species CC-NBS TIR-CC- TIR-NBS- CC-NBS LRR-RLK NBS-LRR NBS -LRR NBS-LRR LRR TIR-NBS Citrullus lanatus Citrus sinensis Fragaria vesca Musa acuminata Morus alba Malus domestica Pyrus bretschneideri Phoenix dactylifera Prunus mume Prunus persica Vitis vinifera Ziziphus jujuba

20 Supplementary Table 29 Unique genes and positively selected genes with NB-ARC domains in the jujube genome IPR ID IPR Title Unique genes and positively selected genes Total number IPR NB-ARC IPR ID reference to the InterPro database 10. Gene IDs addgene2520 addgene2764 addgene2765 addgene2783 addgene2784 addgene3224 addgene3626 addgene3669 CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG CCG Supplementary References 1. Yang, Y. X., Wang, G Y. & Pan, X.Ch. China Food Composition (Book1.2nd Edition) (Peking University Medical Press, 2009). 2. Li, R. et al. The sequence and de novo assembly of the giant panda genome. Nature 463, (2010). 3. Velasco, R. et al. The genome of the domesticated apple (Malus x domestica Borkh.). Nat Genet 42, (2010). 4. Wu, J. et al. The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res 23, (2013). 5. International Peach Genome, I. et al. The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet 45, (2013). 6. Shulaev, V. et al. The genome of woodland strawberry (Fragaria vesca). Nat Genet 43, (2011). 7. Zhang, Q. et al. The genome of Prunus mume. Nat Commun 3, 1318 (2012). 8. He, N. et al. Draft genome sequence of the mulberry tree Morus notabilis. Nat Commun 4, 2445 (2013). 9. Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5, (2008). 10.Hunter, S. et al. InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res 40, (2012).

Supplementary Table 1. Summary of whole genome shotgun sequence used for genome assembly

Supplementary Tables Supplementary Table 1. Summary of whole genome shotgun sequence used for genome assembly Library Read length Raw data Filtered data insert size (bp) * Total Sequence depth Total Sequence