Closed edoardobertolini closed 3 years ago
eweitz
commented
4 years ago Sure! Cytogenetic band data for maize is in zea-mays.json.
Relevant upstream files include genomaize.py and zea-mays-b73-v2-centromeres.tsv. Ideogram added cytogenetic band data for maize in 2017, via #87.
If more would help, please let me know.
edoardobertolini
commented
4 years ago Thanks, Eric! I assume that cytogenetic band coordinates are from the maize assembly AGPv4 and that the centromere coordinates are from the assembly AGPv2. Is this correct? I have reorganized your zea-mays.json according to UCSC format (pasted below) in case others need this data too.
Edo
chrom chromStart chromEnd name gieStain 1 1 2313315 pctg1 gpos25 1 2313316 3568908 pctg2 gneg 1 3568909 6067531 pctg3 gpos25 1 6067532 10072434 pctg4 gneg 1 10072435 13141317 pctg5 gpos25 1 13141318 16417563 pctg6 gneg 1 16417564 17365478 pctg7 gpos25 1 17365479 23480413 pctg8 gneg 1 23480414 29767988 pctg9 gpos25 1 29767989 48177687 pctg10 gneg 1 48177688 52331565 pctg12 gpos25 1 52331566 53064979 pctg13 gneg 1 53064980 65754158 pctg14 gpos25 1 65754159 66917109 pctg445 gneg 1 66917110 67602506 pctg474 gpos25 1 67602507 69547670 pctg16 gneg 1 69547671 71897982 pctg17 gpos25 1 71897983 74744257 pctg18 gneg 1 74744258 79599101 pctg19 gpos25 1 79599102 85903346 pctg20 gneg 1 85903347 87844868 pctg22 gpos25 1 87844869 92198180 pctg23 gneg 1 92198181 95870338 pctg24 gpos25 1 95870339 101871111 pctg26 gneg 1 101871112 108821478 pctg27 gpos25 1 108821479 117626162 pctg28 gneg 1 117626163 124937595 pctg29 gpos25 1 124937596 127161658 pctg471 gneg 1 127161659 134399999 pctg433 gpos25 1 148187334 155060973 qctg31 gneg 1 155060974 160246638 qctg32 gpos25 1 135000001 161331440 qctg480 gneg 1 161331441 161628434 qctg709 gpos25 1 161628435 168879919 qctg33 gneg 1 168879920 177795393 qctg36 gneg 1 177795394 183804760 qctg37 gpos25 1 183804761 184627852 qctg15 gneg 1 184627853 190804281 qctg38 gpos25 1 190804282 192610626 qctg39 gneg 1 192610627 194418632 qctg40 gpos25 1 194418633 202675963 qctg41 gneg 1 202675964 203061654 qctg475 gpos25 1 203061655 204634801 qctg42 gneg 1 204634802 208058421 qctg43 gpos25 1 208058422 221914388 qctg44 gneg 1 221914389 223214444 qctg45 gpos25 1 223214445 223626999 qctg492 gneg 1 223627000 234523618 qctg46 gpos25 1 234523619 237859470 qctg48 gneg 1 237859471 244907521 qctg49 gpos25 1 244907522 250076645 qctg50 gneg 1 250076646 253248259 qctg52 gpos25 1 253248260 254933174 qctg51 gneg 1 254933175 260903138 qctg54 gpos25 1 260903139 279445739 qctg56 gneg 1 279445740 279741197 qctg59 gpos25 1 279741198 281776471 qctg60 gneg 1 281776472 283573620 qctg61 gpos25 1 283573621 287952614 qctg62 gneg 1 287952615 299409530 qctg63 gpos25 1 299409531 301433382 qctg67 gneg 2 1 532094 pctg485 gpos25 2 532095 3692044 pctg68 gneg 2 3692045 7060184 pctg69 gpos25 2 7060185 11230073 pctg70 gneg 2 11230074 14260280 pctg71 gpos25 2 14260281 16759324 pctg72 gneg 2 16759325 17367276 pctg712 gpos25 2 17367277 29703499 pctg74 gneg 2 29703500 30047259 pctg75 gpos25 2 30047260 34205959 pctg76 gneg 2 34205960 41522747 pctg77 gpos25 2 41522748 49998895 pctg78 gneg 2 49998896 50447787 pctg483 gpos25 2 50447788 58077886 pctg79 gneg 2 58077887 64079531 pctg80 gpos25 2 64079532 66127790 pctg81 gneg 2 66127791 68443927 pctg451 gpos25 2 68443928 79506453 pctg82 gneg 2 79506454 81571291 pctg302 gpos25 2 81571292 83204675 pctg83 gneg 2 83204676 84067875 pctg426 gpos25 2 84067876 84769995 pctg85 gneg 2 84769996 92899999 pctg130 gpos25 2 98972614 116453131 qctg86 gneg 2 116453132 118851907 qctg467 gpos25 2 94700001 137166171 qctg89 gneg 2 137166172 172089007 qctg90 gpos25 2 172089008 175817158 qctg92 gneg 2 175817159 176222204 qctg88 gpos25 2 176222205 177803029 qctg95 gneg 2 177803030 178124627 qctg93 gpos25 2 178124628 184101643 qctg96 gneg 2 184101644 185056707 qctg97 gpos25 2 185056708 191405930 qctg98 gneg 2 191405931 193468707 qctg99 gpos25 2 193468708 195452114 qctg100 gneg 2 195452115 197166790 qctg101 gpos25 2 197166791 198254923 qctg102 gneg 2 198254924 205720938 qctg103 gpos25 2 205720939 217445808 qctg104 gneg 2 217445809 220441764 qctg105 gpos25 2 220441765 221478266 qctg107 gneg 2 221478267 231709084 qctg108 gpos25 2 231709085 235490038 qctg109 gneg 2 235490039 235644737 qctg639 gpos25 2 235644738 237893627 qctg110 gneg 3 1 8120190 pctg111 gpos25 3 8120191 11982977 pctg112 gneg 3 11982978 19015255 pctg113 gpos25 3 19015256 27529319 pctg115 gneg 3 27529320 46889799 pctg117 gpos25 3 46889800 56546115 pctg118 gneg 3 56546116 64514003 pctg119 gpos25 3 64514004 82839601 pctg120 gneg 3 82839602 99699999 pctg730 gpos25 3 113255632 125064082 qctg122 gneg 3 125064083 141247510 qctg124 gpos25 3 100700001 147279871 qctg126 gneg 3 147279872 152439451 qctg128 gpos25 3 152439452 155769959 qctg129 gneg 3 155769960 174353644 qctg131 gpos25 3 174353645 176871575 qctg134 gneg 3 176871576 179284579 qctg135 gpos25 3 179284580 181585898 qctg136 gneg 3 181585899 194189154 qctg138 gpos25 3 194189155 196358092 qctg140 gneg 3 196358093 200243259 qctg141 gpos25 3 200243260 202576128 qctg142 gneg 3 202576129 204504304 qctg143 gpos25 3 204504305 205335064 qctg144 gneg 3 205335065 214307228 qctg145 gpos25 3 214307229 217203188 qctg147 gneg 3 217203189 220814237 qctg149 gpos25 3 220814238 226274536 qctg150 gneg 3 226274537 230653959 qctg151 gpos25 3 230653960 231891516 qctg152 gneg 3 231891517 232227970 qctg153 gpos25 4 1 1349462 pctg154 gneg 4 1349463 1518061 pctg702 gpos25 4 1518062 4135806 pctg155 gneg 4 4135807 11324719 pctg156 gpos25 4 11324720 14268296 pctg158 gneg 4 14268297 16044453 pctg159 gpos25 4 16044454 22798922 pctg160 gneg 4 22798923 23669946 pctg531 gpos25 4 23669947 27276238 pctg162 gneg 4 27276239 31458684 pctg163 gpos25 4 31458685 47285273 pctg164 gneg 4 47285274 50430753 pctg435 gpos25 4 50430754 55443723 pctg190 gneg 4 55443724 62095577 pctg165 gpos25 4 62095578 67716356 pctg166 gneg 4 67716357 77809335 pctg172 gpos25 4 77809336 80975362 pctg174 gneg 4 80975363 83853967 pctg168 gpos25 4 83853968 85129659 pctg444 gneg 4 85129660 96840250 pctg169 gpos25 4 96840251 105299999 pctg183 gneg 4 114067851 129021032 qctg171 gpos25 4 129021033 132425205 qctg173 gneg 4 106100001 134238207 qctg175 gpos25 4 134238208 141923594 qctg176 gneg 4 141923595 149548121 qctg179 gpos25 4 149548122 152068542 qctg246 gneg 4 152068543 159750699 qctg181 gpos25 4 159750700 181984697 qctg182 gneg 4 181984698 182124566 qctg545 gpos25 4 182124567 187388089 qctg184 gneg 4 187388090 188234079 qctg185 gpos25 4 188234080 188539418 qctg186 gneg 4 188539419 190507692 qctg187 gpos25 4 190507693 199141608 qctg188 gneg 4 199141609 200421705 qctg191 gpos25 4 200421706 203020057 qctg194 gneg 4 203020058 209139284 qctg193 gpos25 4 209139285 211606081 qctg469 gneg 4 211606082 211963774 qctg697 gpos25 4 211963775 213364855 qctg192 gneg 4 213364856 215485757 qctg195 gpos25 4 215485758 219434627 qctg127 gneg 4 219434628 225131713 qctg196 gpos25 4 225131714 225722842 qctg482 gneg 4 225722843 231549779 qctg199 gpos25 4 231549780 233471777 qctg198 gneg 4 233471778 235906895 qctg200 gpos25 4 235906896 238998537 qctg201 gneg 4 238998538 240877213 qctg202 gpos25 4 240877214 242029974 qctg203 gneg 5 1 5480922 pctg204 gpos25 5 5480923 5919179 pctg205 gneg 5 5919180 7982490 pctg206 gpos25 5 7982491 11745108 pctg207 gneg 5 11745109 14453672 pctg209 gpos25 5 14453673 17191388 pctg210 gneg 5 17191389 18007842 pctg460 gpos25 5 18007843 20803742 pctg211 gneg 5 20803743 28691747 pctg212 gpos25 5 28691748 29228197 pctg698 gneg 5 29228198 31172592 pctg215 gpos25 5 31172593 31938581 pctg216 gneg 5 31938582 38510291 pctg217 gpos25 5 38510292 45994885 pctg218 gneg 5 45994886 46535779 pctg486 gpos25 5 46535780 55350536 pctg219 gneg 5 55350537 62708481 pctg220 gpos25 5 62708482 65017546 pctg221 gneg 5 65017547 77748588 pctg223 gpos25 5 77748589 89387911 pctg225 gneg 5 89387912 95178670 pctg227 gpos25 5 95178671 102299999 pctg228 gneg 5 122068152 124279005 qctg230 gpos25 5 124279006 127328484 qctg494 gneg 5 109200001 130509989 qctg233 gpos25 5 130509990 161721095 qctg234 gneg 5 161721096 163895815 qctg237 gpos25 5 163895816 178843541 qctg238 gneg 5 178843542 179916115 qctg241 gpos25 5 179916116 183702968 qctg242 gneg 5 183702969 186946371 qctg244 gpos25 5 186946372 190742387 qctg245 gneg 5 190742388 195160688 qctg247 gpos25 5 195160689 195330276 qctg715 gneg 5 195330277 195474639 qctg500 gpos25 5 195474640 195643556 qctg248 gneg 5 195643557 197355011 qctg249 gpos25 5 197355012 205139749 qctg250 gneg 5 205139750 208228772 qctg251 gpos25 5 208228773 213273550 qctg253 gneg 5 213273551 217928451 qctg254 gpos25 6 1 2127033 pctg256 gneg 6 2127034 5303120 pctg257 gpos25 6 5303121 6157706 pctg259 gneg 6 6157707 10090842 pctg260 gpos25 6 10090843 13183877 pctg438 gneg 6 13183878 15943428 pctg263 gpos25 6 15943429 20721503 pctg264 gneg 6 20721504 23832598 pctg261 gpos25 6 23832599 36069255 pctg262 gneg 6 36069256 39148192 pctg268 gpos25 6 39148193 39307471 pctg665 gneg 6 39307472 49599999 pctg267 gpos25 6 63758519 65105257 qctg442 gneg 6 65105258 76596340 qctg269 gpos25 6 50000001 84973091 qctg270 gneg 6 84973092 93618543 qctg271 gpos25 6 93618544 95492039 qctg272 gneg 6 95492040 97815292 qctg273 gpos25 6 97815293 103957049 qctg274 gneg 6 103957050 106943298 qctg276 gpos25 6 106943299 110137540 qctg280 gneg 6 110137541 111309336 qctg277 gpos25 6 111309337 111931577 qctg477 gneg 6 111931578 129234376 qctg281 gpos25 6 129234377 132123932 qctg282 gneg 6 132123933 140136457 qctg283 gpos25 6 140136458 142388006 qctg284 gneg 6 142388007 149924898 qctg285 gpos25 6 149924899 150775227 qctg286 gneg 6 150775228 164118346 qctg287 gpos25 6 164118347 167771369 qctg289 gneg 6 167771370 169381756 qctg291 gpos25 7 1 714032 pctg714 gneg 7 714033 1062466 pctg292 gpos25 7 1062467 3646467 pctg293 gneg 7 3646468 5264773 pctg294 gpos25 7 5264774 5401381 pctg295 gneg 7 5401382 6291179 pctg487 gpos25 7 6291180 14708138 pctg296 gneg 7 14708139 19454947 pctg297 gpos25 7 19454948 22729593 pctg298 gneg 7 22729594 31652190 pctg299 gpos25 7 31652191 38930597 pctg300 gneg 7 38930598 51542694 pctg301 gpos25 7 51542695 54599999 pctg303 gneg 7 67940937 71310639 qctg459 gneg 7 71310640 78893005 qctg470 gpos25 7 78893006 85282835 qctg304 gneg 7 62500001 85412767 qctg719 gpos25 7 85412768 92459409 qctg306 gneg 7 92459410 93359709 qctg308 gpos25 7 93359710 98434784 qctg307 gneg 7 98434785 110707691 qctg309 gpos25 7 110707692 113633161 qctg311 gneg 7 113633162 117261655 qctg312 gpos25 7 117261656 120752894 qctg313 gneg 7 120752895 123588031 qctg315 gpos25 7 123588032 125522865 qctg316 gneg 7 125522866 125817467 qctg452 gpos25 7 125817468 128038288 qctg317 gneg 7 128038289 138227912 qctg318 gpos25 7 138227913 150237214 qctg320 gneg 7 150237215 162212420 qctg322 gpos25 7 162212421 162722287 qctg324 gneg 7 162722288 176810253 qctg325 gpos25 8 1 16228641 pctg326 gneg 8 16228642 17604173 pctg327 gpos25 8 17604174 19042351 pctg328 gneg 8 19042352 26171690 pctg329 gpos25 8 26171691 27338692 pctg341 gneg 8 27338693 32291022 pctg330 gpos25 8 32291023 37807736 pctg331 gneg 8 37807737 45235680 pctg334 gpos25 8 45235681 47052700 pctg457 gneg 8 47052701 48999999 pctg429 gpos25 8 55524039 59318823 qctg343 gpos25 8 51400001 63105063 qctg333 gneg 8 63105064 64219682 qctg335 gpos25 8 64219683 72316516 qctg336 gneg 8 72316517 74348353 qctg339 gpos25 8 74348354 81133562 qctg344 gneg 8 81133563 86033697 qctg338 gpos25 8 86033698 87062963 qctg337 gneg 8 87062964 96848924 qctg340 gpos25 8 96848925 102026214 qctg345 gneg 8 102026215 103708881 qctg346 gpos25 8 103708882 106489423 qctg347 gneg 8 106489424 109104805 qctg348 gpos25 8 109104806 116550835 qctg349 gneg 8 116550836 120824083 qctg350 gpos25 8 120824084 122265092 qctg352 gneg 8 122265093 125032496 qctg353 gpos25 8 125032497 138288132 qctg354 gneg 8 138288133 139263340 qctg355 gpos25 8 139263341 142466043 qctg356 gneg 8 142466044 155703284 qctg358 gpos25 8 155703285 160168698 qctg360 gneg 8 160168699 164232557 qctg362 gpos25 8 164232558 169558891 qctg363 gneg 8 169558892 171293270 qctg364 gpos25 8 171293271 171721914 qctg365 gneg 8 171721915 175347686 qctg366 gpos25 9 1 975459 pctg441 gneg 9 975460 8427952 pctg368 gpos25 9 8427953 9225506 pctg369 gneg 9 9225507 12749618 pctg370 gpos25 9 12749619 12947586 pctg484 gneg 9 12947587 13366954 pctg372 gpos25 9 13366955 28960374 pctg373 gneg 9 28960375 30352892 pctg490 gpos25 9 30352893 31560478 pctg381 gneg 9 31560479 32551216 pctg453 gpos25 9 32551217 35696590 pctg377 gneg 9 35696591 38570305 pctg378 gpos25 9 38570306 44268913 pctg367 gneg 9 44268914 47883849 pctg374 gpos25 9 47883850 52425569 pctg375 gneg 9 52425570 54138261 pctg425 gpos25 9 54138262 56178103 pctg214 gneg 9 56178104 62946627 pctg106 gpos25 9 62946628 63630814 pctg491 gneg 9 63630815 64299102 pctg450 gpos25 9 64299103 68959128 pctg432 gneg 9 68959129 72199999 pctg703 gpos25 9 73715208 83063646 qctg197 gpos25 9 72700001 84026052 qctg431 gneg 9 84026053 106887131 qctg376 gpos25 9 106887132 107421808 qctg499 gneg 9 107421809 109844390 qctg380 gpos25 9 109844391 111053757 qctg473 gneg 9 111053758 111394837 qctg707 gpos25 9 111394838 114645517 qctg382 gneg 9 114645518 121051048 qctg383 gpos25 9 121051049 121775804 qctg458 gpos25 9 121775805 123242411 qctg384 gneg 9 123242412 131501217 qctg385 gpos25 9 131501218 134124167 qctg386 gneg 9 134124168 139834530 qctg387 gpos25 9 139834531 140795148 qctg388 gneg 9 140795149 146965649 qctg389 gpos25 9 146965650 148616820 qctg390 gneg 9 148616821 157021084 qctg391 gpos25 10 1 510750 pctg519 gneg 10 510751 6415486 pctg392 gpos25 10 6415487 11346032 pctg393 gneg 10 11346033 14687260 pctg394 gpos25 10 14687261 23957819 pctg395 gneg 10 23957820 26504604 pctg397 gpos25 10 26504605 50099999 pctg398 gneg 10 60810162 69333048 qctg400 gpos25 10 69333049 76145432 qctg401 gneg 10 52400001 78871909 qctg402 gpos25 10 78871910 82207630 qctg403 gneg 10 82207631 84261873 qctg404 gpos25 10 84261874 85490282 qctg405 gneg 10 85490283 89198279 qctg406 gpos25 10 89198280 91903517 qctg408 gneg 10 91903518 98138774 qctg409 gpos25 10 98138775 100028090 qctg410 gneg 10 100028091 113177895 qctg411 gpos25 10 113177896 113611229 qctg721 gneg 10 113611230 121272978 qctg412 gpos25 10 121272979 133117406 qctg413 gneg 10 133117407 139262074 qctg414 gpos25 10 139262075 140586583 qctg416 gneg 10 140586584 143672659 qctg417 gpos25 10 143672660 144800078 qctg418 gneg 10 144800079 148157518 qctg419 gpos25 10 148157519 149627545 qctg420 gneg
Il giorno lun 9 nov 2020 alle ore 13:41 Eric Weitz notifications@github.com ha scritto:
Sure! Here it is: https://raw.githubusercontent.com/eweitz/ideogram/master/data/bands/native/zea-mays.json .
Relevant upstream files include genomaize.py https://github.com/eweitz/ideogram/blob/5c6c5578b93bda3013034be2eef1c0e8c7b8fb6f/scripts/python/fetch_chromosomes/genomaize.py and zea-mays-b73-v2-centromeres.tsv https://raw.githubusercontent.com/eweitz/ideogram/5c6c5578b93bda3013034be2eef1c0e8c7b8fb6f/dist/data/bands/native/zea-mays-b73-v2-centromeres.tsv. Ideogram added cytogenetic band data for maize in 2017, via #87 https://github.com/eweitz/ideogram/pull/87.
If more would help, please let me know.
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eweitz
commented
4 years ago Much appreciated, Edo. Any chance you could open a PR with that data?
eweitz
commented
4 years ago cytogenetic band coordinates are from the maize assembly AGPv4 and that the centromere coordinates are from the assembly AGPv2. Is this correct?
~Not quite. Bands and centromeres are both from AGPv2.~ (See next comment for clarifications.)
More specifically, ~bands and~ centromeres are from zeaMay_b73_v2 in Genomaize, which per MaizeGDB is also known as AGPv2, formally B73 RefGen_v2 (GCA_000005005.4).
I'll keep this issue open for a week or so, in case you can open a PR with your UCSC-formatted data.
eweitz
commented
3 years ago (Below is adapted from an email I sent. I surface it here for any future curious maize researchers.)
Investigating deeper, I see my previous comment has an error. Ideogram.js data for Zea mays (maize, corn) centromeres is indeed from Genomaize [1], but its "bands" are from Ensembl [2]. Specifically, the maize cytobands came from Ensembl's public MySQL database zea_mays_core_35_88_7. That database no longer exists, but an earlier archive shows a "bands" column in a "karyotype" table. Detailed steps to reproduce, and full raw output, are shown below in [3].
You can also access similar data more simply, at ftp://ftp.ensemblgenomes.org/pub/plants/release-25/mysql/zea_mays_core_25_78_6/karyotype.txt.gz. That link comes by way of https://www.biostars.org/p/240614/. It's unfortunate that such data is not available for new assembly versions; I suspect it was deprioritized due to lack a way for Ensembl to visualize the data. Ideogram.js is the only resource I know that shows maize centromeres and bands (https://eweitz.github.io/ideogram/eukaryotes?org=zea-mays).
The experimental origin of such band data would certainly help to know. I see a 1985 paper notes "different classes of maize heterochromatin can be differentiated through C-banding" [4].
The paper discusses knobs and other heterochromatin patterns -- perhaps the Ensembl "bands" represent the latter?
[1] Specifically, from:
Ideogram code: https://github.com/eweitz/ideogram/blob/5c6c5578b93bda3013034be2eef1c0e8c7b8fb6f/scripts/python/fetch_chromosomes/genomaize.py
[2] See query_ensembl_karyotype_db in Ideogram cytogenetics pipeline:
[3] To reproduce, run commands below on a computer with mysql installed.
$ mysql --host mysql-eg-publicsql.ebi.ac.uk --port 4157 --user anonymous -A
Welcome to the MySQL monitor. Commands end with ; or \g.
Your MySQL connection id is 5063862
Server version: 5.6.33 MySQL Community Server (GPL)
Copyright (c) 2000, 2017, Oracle and/or its affiliates. All rights reserved.
Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective
owners.
Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.
mysql> use zea_mays_core_29_82_6;
Database changed
mysql> select * from karyotype;[4] See page 28 in "C-banding in Maize. I. Band patterns", by De Aguiar Perecin. https://www.researchgate.net/publication/283587917_C-Banding_in_Maize_I_Band_Patterns
eweitz
commented
3 years ago I'll close this for now, but would still welcome a PR with UCSC-formatted data!
Hello Eric, Could you please share the cytogenetic band data for the species Zea mays (corn). I cannot retrieve the data from Genomaize. Thanks! Edo