Rice Chromosome 3 Supplemental Data

Rice Chromosome 3 Supplemental Data

Page 21

Supplemental Data

Supplementary Table 1. Repetitive sequences on japonica chromosome 3. The rice chromosome 3 pseudomolecule was searched against the TIGR Oryza Repeat database using RepeatMasker with a cutoff score of 225. Each sub-class was collapsed and quantitated.

Classification / Total length (kp) / Percent in repeat fraction / Percent in dataset / Occurrence / Occurrence (per Mb) / Average size (bp)
Transposable elements / 7,073.01 / 91.72% / 19.59% / 18,941 / 524.64 / 373.42
Retrotransposons
Ty1-copia / 442.17 / 5.73% / 1.22% / 376 / 10.41 / 1,175.98
Ty3-gypsy / 1,640.30 / 21.27% / 4.54% / 1,101 / 30.50 / 1,489.82
LINE / 13.30 / 0.17% / 0.04% / 23 / 0.64 / 578.39
Unclassified Retrotransposons / 1,283.79 / 16.65% / 3.56% / 1,245 / 34.48 / 1,031.15
Subtotal (Retrotransposons) / 3,379.55 / 43.82% / 9.36% / 2,745 / 76.03 / 1,231.17
Transposons
Ac/Ds / 18.30 / 0.24% / 0.05% / 123 / 3.41 / 148.80
CACTA, En/Spm / 679.57 / 8.81% / 1.88% / 841 / 23.29 / 808.05
Mutator (MULE) / 85.91 / 1.11% / 0.24% / 372 / 10.30 / 230.94
Mariner (MLE) / 10.23 / 0.13% / 0.03% / 22 / 0.61 / 465.05
ping/pong/SNOOPY / 6.20 / 0.08% / 0.02% / 15 / 0.42 / 413.07
Unclassified Transposons / 601.29 / 7.80% / 1.67% / 2,958 / 81.93 / 203.28
Subtotal (Transposons) / 1,401.50 / 18.17% / 3.88% / 4,331 / 119.96 / 323.60
MITEs
Tourist / 335.40 / 4.35% / 0.93% / 1,254 / 34.73 / 267.46
Stowaway / 3.33 / 0.04% / 0.01% / 37 / 1.02 / 89.92
Crackle / 41.37 / 0.54% / 0.11% / 189 / 5.24 / 218.90
Explorer / 34.98 / 0.45% / 0.10% / 278 / 7.70 / 125.84
Gaijin/Gaigin / 112.53 / 1.46% / 0.31% / 777 / 21.52 / 144.83
Castaway / 123.96 / 1.61% / 0.34% / 464 / 12.85 / 267.16
Snap / 16.23 / 0.21% / 0.04% / 97 / 2.69 / 167.32
Amy/LTP / 17.53 / 0.23% / 0.05% / 58 / 1.61 / 302.19
Ditto / 134.67 / 1.75% / 0.37% / 625 / 17.31 / 215.48
Wanderer / 58.65 / 0.76% / 0.16% / 378 / 10.47 / 155.17
p-SINE1 / 39.92 / 0.52% / 0.11% / 263 / 7.28 / 151.78
Pop / 12.94 / 0.17% / 0.04% / 123 / 3.41 / 105.18
Krispie / 0.37 / 0.00% / 0.00% / 2 / 0.06 / 183.00
Snabo / 43.33 / 0.56% / 0.12% / 237 / 6.56 / 182.82
MITE-adh, type A / 84.90 / 1.10% / 0.24% / 432 / 11.97 / 196.52
MITE-adh, type B / 342.77 / 4.44% / 0.95% / 1,617 / 44.79 / 211.98
MITE-adh, type D / 122.40 / 1.59% / 0.34% / 1,018 / 28.20 / 120.24
MITE-adh, type G / 32.01 / 0.42% / 0.09% / 132 / 3.66 / 242.46
MITE-adh, type H / 17.38 / 0.23% / 0.05% / 66 / 1.83 / 263.36
MITE-adh, type I / 111.06 / 1.44% / 0.31% / 628 / 17.39 / 176.85
MITE-adh, type J / 44.06 / 0.57% / 0.12% / 395 / 10.94 / 111.56
MITE-adh, type K / 64.57 / 0.84% / 0.18% / 412 / 11.41 / 156.73
MITE-adh, type L / 22.92 / 0.30% / 0.06% / 123 / 3.41 / 186.34
MITE-adh, type M / 42.90 / 0.56% / 0.12% / 238 / 6.59 / 180.23
MITE-adh, type N / 5.26 / 0.07% / 0.01% / 36 / 1.00 / 146.17
MITE-adh-1 / 1.08 / 0.01% / 0.00% / 8 / 0.22 / 135.38
MITE-adh-2 / 8.42 / 0.11% / 0.02% / 40 / 1.11 / 210.53
MITE-adh-3 / 5.47 / 0.07% / 0.02% / 32 / 0.89 / 170.84
MITE-adh-4 / 13.59 / 0.18% / 0.04% / 76 / 2.11 / 178.80
MITE-adh-5 / 90.01 / 1.17% / 0.25% / 347 / 9.61 / 259.39
MITE-adh-6 / 0.51 / 0.01% / 0.00% / 3 / 0.08 / 168.67
MITE-adh-8 / 8.46 / 0.11% / 0.02% / 62 / 1.72 / 136.42
MITE-adh-9 / 11.98 / 0.16% / 0.03% / 71 / 1.97 / 168.76
MITE-adh-10 / 3.89 / 0.05% / 0.01% / 27 / 0.75 / 144.00
MITE-adh-11 / 41.90 / 0.54% / 0.12% / 100 / 2.77 / 419.00
MITE-adh-12 / 0.87 / 0.01% / 0.00% / 5 / 0.14 / 173.20
Buhui / 15.74 / 0.20% / 0.04% / 60 / 1.66 / 262.40
Casin / 1.62 / 0.02% / 0.00% / 12 / 0.33 / 135.33
Centre / 6.71 / 0.09% / 0.02% / 40 / 1.11 / 167.72
Delay / 2.92 / 0.04% / 0.01% / 16 / 0.44 / 182.62
ECR / 12.91 / 0.17% / 0.04% / 64 / 1.77 / 201.70
Helia / 3.90 / 0.05% / 0.01% / 26 / 0.72 / 150.08
ID-2 / 1.63 / 0.02% / 0.00% / 8 / 0.22 / 203.25
ID-3 / 13.25 / 0.17% / 0.04% / 68 / 1.88 / 194.91
ID-4 / 7.45 / 0.10% / 0.02% / 42 / 1.16 / 177.38
Lier / 1.86 / 0.02% / 0.01% / 13 / 0.36 / 143.08
Stola / 9.24 / 0.12% / 0.03% / 33 / 0.91 / 280.00
Stone / 0.11 / 0.00% / 0.00% / 1 / 0.03 / 109.00
Susu / 11.56 / 0.15% / 0.03% / 45 / 1.25 / 256.98
Wuji / 0.40 / 0.01% / 0.00% / 5 / 0.14 / 80.20
Youren / 16.69 / 0.22% / 0.05% / 72 / 1.99 / 231.75
Micron / 54.27 / 0.70% / 0.15% / 280 / 7.76 / 193.81
Pangrangja / 59.95 / 0.78% / 0.17% / 319 / 8.84 / 187.94
Kiddo / 5.37 / 0.07% / 0.01% / 34 / 0.94 / 158.00
mPing/miniSNOOPY / 4.30 / 0.06% / 0.01% / 10 / 0.28 / 430.00
MDM / 10.45 / 0.14% / 0.03% / 67 / 1.86 / 155.99
Subtotal (MITEs) / 2,291.96 / 29.72% / 6.35% / 11,865 / 328.65 / 193.17
Centromere-related
Centromere-specific Retrotransposon / 118.75 / 1.54% / 0.33% / 262 / 7.26 / 453.24
CentO / 48.60 / 0.63% / 0.13% / 123 / 3.41 / 395.15
Unclassified Centromere Sequences / 20.53 / 0.27% / 0.06% / 56 / 1.55 / 366.54
Subtotal (Centromere-related) / 187.88 / 2.44% / 0.52% / 441 / 12.22 / 426.03
Telomere-related
Telomere-associated / 5.14 / 0.07% / 0.01% / 20 / 0.55 / 257.25
Telomere / 0.21 / 0.00% / 0.00% / 3 / 0.08 / 71.67
Subtotal (Telomere-related) / 5.36 / 0.07% / 0.01% / 23 / 0.64 / 233.04
Ribosomal RNA genes
45S rDNA / 12.49 / 0.16% / 0.03% / 50 / 1.38 / 249.78
5S rDNA / 4.16 / 0.05% / 0.01% / 59 / 1.63 / 70.53
Subtotal (Ribosomal RNA genes) / 16.65 / 0.22% / 0.05% / 109 / 3.02 / 152.75
Unclassified / 428.84 / 5.56% / 1.19% / 1,968 / 54.51 / 217.90
Total / 7,711.74 / 100.00% / 21.36% / 21,482 / 595.03

Supplementary Table 2. Putative orthologs and paralogs of japonica chromosome 3 proteins in other model species. All 6,232 predicted proteins from japonica chromosome 3 were searched against the predicted proteomes of E. coli, Synechocystis, yeast, fly, worm, Arabidopsis and human using BLASTP. The matches were parsed out based on BLASTP E-value cutoff of 10-5.

E value / Arabidopsis / Yeast / C.elegans / Fly / Human / Synechocystis / E. coli
e-200 / 440 / 22 / 32 / 34 / 43 / 5 / 2
e-150 to e-200 / 366 / 38 / 48 / 56 / 56 / 8 / 11
e-100 to e-150 / 622 / 99 / 84 / 90 / 110 / 38 / 24
e-50 to e-100 / 1,081 / 276 / 347 / 283 / 347 / 124 / 111
e-10 to e-50 / 1,260 / 1,034 / 1,161 / 1,087 / 1,272 / 512 / 351
e-5 to e-10 / 432 / 541 / 672 / 687 / 699 / 338 / 241
Total matched / 4,201 / 2,010 / 2,344 / 2,237 / 2,527 / 1,025 / 740
Total protein in dataset / 28,952 / 6,700 / 22,259 / 18,746 / 27,175 / 3,167 / 5,361
Percent Matched / 67.4 / 32.3 / 37.6 / 35.9 / 40.6 / 16.4 / 11.9

Rice Chromosome 3 Supplemental Data

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Supplementary Table 3. Predominant Pfam domains within the predicted japonica chromosome 3 proteome. All non-TE related proteins were searched with the HMMer program and Pfam domains above the trusted cutoff were parsed out. Only the top 20 Pfam domains are listed.

Pfam accession / No. of
Matched Proteins / Pfam domain
PF00069 / 127 / Protein kinase domain
PF01535 / 69 / PPR repeat
PF00646 / 63 / F-box domain
PF00560 / 57 / Leucine Rich Repeat
PF00076 / 44 / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
PF00400 / 40 / WD domain, G-beta repeat
PF00097 / 36 / Zinc finger, C3HC4 type (RING finger)
PF00249 / 32 / Myb-like DNA-binding domain
PF00067 / 31 / Cytochrome P450
PF00023 / 25 / Ankyrin repeat
PF00271 / 23 / Helicase conserved C-terminal domain
PF00226 / 22 / DnaJ domain
PF00010 / 21 / Helix-loop-helix DNA-binding domain
PF00036 / 21 / EF hand
PF00096 / 21 / Zinc finger, C2H2 type
PF00515 / 21 / TPR Domain
PF00141 / 20 / Peroxidase
PF00234 / 20 / Protease inhibitor/seed storage/LTP family
PF00847 / 19 / AP2 domain
PF00931 / 19 / NB-ARC domain

Supplementary Table 4. Coverage of japonica chromosome 3 by O. nivara BAC clones.

Contig / Start on O. sativa chr3 / Stop on O. sativa chr3 / Contig length
(bp) / Gap length
(bp)
Contig 1 / 8679 / 5163796 / 5155117
3272
Contig 2 / 5167068 / 6796965 / 1629897
36446
Contig 3 / 6833411 / 12541419 / 5708008
419878
Contig 4 / 12961297 / 14183439 / 1222142
15194
Contig 5 / 14198633 / 16189765 / 1991132
2519
Contig 6 / 16192284 / 19347517 / 3155233
CEN
Contig 7 / 19292806 / 20721690 / 1428884
53299
Contig 8 / 20774989 / 23748502 / 2973513
23735
Contig 9 / 23772237 / 24708967 / 936730
491152
Contig 10 / 25200119 / 27037097 / 1836978
29218
Contig 11 / 27066315 / 28562962 / 1496647
22072
Contig 12 / 28585034 / 31810098 / 3225064
10102
Contig 13 / 31820200 / 32807999 / 987799
5622
Contig 14 / 32813621 / 33869384 / 1055763
16171
Contig 15 / 33885555 / 34914872 / 1029317
27168
Contig 16 / 34942040 / 36097741 / 1155701
Total / 34987925 / 1155848

Supplementary Table 5. Summary of size and content of insertion/deletion/null blocks, relative to the O. nivara chromosome 3 FPC map, using a 200kb sliding window across the japonica chromosome 3 pseudomolecule.

200kb window / Number of Blocks / Block size (Mb) / Repeat content (%) / Paralogs/ gene (%)
Insertion block / 106 / 34 / 21.2 / 21.7 / 46.1
Same size block / 67 / 36 / 13.4 / 24.1 / 43.9
Deletion block / 2 / 2 / 0.4 / 42.6 / 36.8

Supplementary Table 6. Summary of SSR frequencies by repeat classes among the japonica genome, japonica chromosome 3, the indica genome and O. nivara BAC end sequences.

SSR Type(%) / japonica genome / japonica
Chr3 / indica WGS / O. nivara BES
di / 19.15 / 20.73 / 22.62 / 22.55
tri / 57.68 / 57.05 / 53.46 / 55.71
tetra / 7.87 / 7.72 / 8.55 / 8.34
penta / 12.17 / 11.51 / 12.09 / 9.59
hexa / 3.12 / 2.99 / 3.29 / 3.81

Rice Chromosome 3 Supplemental Data

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Supplementary Table 7. Polymorphic SSRs identified by comparison of O. nivara with O. sativa spp. japonica.

Repeat / SSRs / Start / Stop / SSR length / SSR length / Length / SSR-BES
unit / in Chr / in BES / difference / name
4 / CGAG/CTCG / 846549 / 846586 / 38 / 23 / -15 / OR_BBa0021K12.r
OR_BBa0112P19.r
OR_BBa0135L02.r
3 / CCG/CGG / 945896 / 946031 / 136 / 191 / 55 / OR_BBa0115C10.f
3 / CCG/CGG / 1169325 / 1169364 / 40 / 53 / 13 / OR_BBa0081A13.f
3 / CTA/TAG / 1501227 / 1501254 / 28 / 25 / -3 / OR_BBa0091H22.f
3 / CAG/CTG / 2146715 / 2146734 / 20 / 26 / 6 / OR_BBa0067F17.r
2 / TA / 2336002 / 2336051 / 50 / 54 / 4 / OR_BBa0085L08.f
3 / CAA/TTG / 3079909 / 3079944 / 36 / 27 / -9 / OR_BBa0038K22.r
OR_BBa0012J14.f
OR_BBa0059M17.r
OR_BBa0103A08.r
OR_BBa0033G15.f
2 / GA/CT / 3194778 / 3194827 / 50 / 40 / -10 / OR_BBa0119F01.r
2 / TA / 3436131 / 3436182 / 52 / 35 / -17 / OR_BBa0058L14.f
3 / TCG/CGA / 3875025 / 3875078 / 54 / 57 / 3 / OR_BBa0119C08.f
2 / CA/TG / 3965154 / 3965183 / 30 / 38 / 8 / OR_BBa0079B16.r
2 / TA / 4705997 / 4706071 / 75 / 27 / -48 / OR_BBa0039K06.r
OR_BBa0118O22.f
OR_BBa0139K21.f
2 / GA/CT / 4917269 / 4917328 / 60 / 48 / -12 / OR_BBa0004E11.f
2 / GA/CT / 5182384 / 5182410 / 27 / 21 / -6 / OR_BBa0023G08.f
3 / CCG/CGG / 5365625 / 5365653 / 29 / 32 / 3 / OR_BBa0085I22.f
3 / CCG/CGG / 6104485 / 6104554 / 70 / 63 / -7 / OR_BBa0006N15.f
3 / GAA/TTC / 6437560 / 6437589 / 30 / 48 / 18 / OR_BBa0138A22.r
5 / CGAGG/CCTCG / 6615262 / 6615352 / 91 / 20 / -71 / OR_BBa0018H24.f
2 / TA / 7936423 / 7936502 / 80 / 24 / -56 / OR_BBa0126B10.r
2 / GA/CT / 8676429 / 8676448 / 20 / 26 / 6 / OR_BBa0048N24.f
3 / CCG/CGG / 9800266 / 9800285 / 20 / 23 / 3 / OR_BBa0106C14.f
3 / GAA/TTC / 10305406 / 10305436 / 31 / 28 / -3 / OR_BBa0077F21.f
2 / GA/CT / 10330576 / 10330647 / 72 / 48 / -24 / OR_BBa0069M22.r
3 / CCG/CGG / 10344486 / 10344509 / 24 / 21 / -3 / OR_BBa0087H01.r
3 / CAG/CTG / 10745216 / 10745250 / 35 / 32 / -3 / OR_BBa0087H13.r
3 / GGA/TCC / 10885603 / 10885622 / 20 / 23 / 3 / OR_BBa0128J21.r
2 / TA / 11639023 / 11639075 / 53 / 62 / 9 / OR_BBa0127K14.f
OR_BBa0069F14.f
2 / TA / 11655227 / 11655258 / 32 / 180 / 148 / OR_BBa0017E18.f
3 / CCG/CGG / 11828662 / 11828802 / 141 / 25 / -116 / OR_BBa0017J11.r
3 / GGA/TCC / 12258164 / 12258184 / 21 / 24 / 3 / OR_BBa0075C14.r
3 / CCG/CGG / 12519061 / 12519080 / 20 / 23 / 3 / OR_BBa0070P03.f
3 / GAA/TTC / 14346091 / 14346131 / 41 / 71 / 30 / OR_BBa0073G11.f
2 / GA/CT / 15826511 / 15826549 / 39 / 21 / -18 / OR_BBa0028I24.f
3 / CAA/TTG / 16005470 / 16005512 / 43 / 28 / -15 / OR_BBa0032L04.r
3 / CCG/CGG / 16258948 / 16259035 / 88 / 53 / -35 / OR_BBa0132I01.f
6 / TCTCCC/GGGAGA / 17116459 / 17116486 / 28 / 31 / 3 / OR_BBa0120I16.f
3 / TAA/TTA / 17641239 / 17641322 / 84 / 57 / -27 / OR_BBa0071F23.r
2 / TA / 17720541 / 17720590 / 50 / 98 / 48 / OR_BBa0120P24.r
OR_BBa0008A05.f
2 / GA/CT / 17973052 / 17973076 / 25 / 29 / 4 / OR_BBa0121F15.f
OR_BBa0070G17.f
2 / GA/CT / 19224536 / 19224586 / 51 / 47 / -4 / OR_BBa0017D17.r
OR_BBa0126H24.r
3 / CCG/CGG / 19721940 / 19722036 / 97 / 94 / -3 / OR_BBa0129A22.f
3 / GGA/TCC / 20092772 / 20092795 / 24 / 27 / 3 / OR_BBa0009F15.r
2 / TA / 20611027 / 20611058 / 32 / 20 / -12 / OR_BBa0037M14.f
3 / CCG/CGG / 20935516 / 20935650 / 135 / 96 / -39 / OR_BBa0049F22.f
3 / CAA/TTG / 21238653 / 21238689 / 37 / 31 / -6 / OR_BBa0129F20.f
3 / TCG/CGA / 21510710 / 21510729 / 20 / 23 / 3 / OR_BBa0129I22.r
OR_BBa0041M24.r
OR_BBa0093B07.r
3 / GAA/TTC / 22235230 / 22235308 / 79 / 76 / -3 / OR_BBa0134H24.f
OR_BBa0070G09.r
2 / GA/CT / 22615202 / 22615230 / 29 / 36 / 7 / OR_BBa0010H19.r
5 / CCGAG/CTCGG / 22615392 / 22615411 / 20 / 23 / 3 / OR_BBa0010H19.r
3 / CCG/CGG / 22881252 / 22881433 / 182 / 172 / -10 / OR_BBa0105M08.f