Welcome to Cucurbitaceae Information Resource

The Cucurbitaceae Information Resource (CuIR) provides comprehensive services 177 reference genomes from 67 Cucurbitaceae plants, offering genome assemblies, gene models, and annotations. Moreover, 6,815 transcriptome libraries from 26 species were collected, analyzed, and deposited in CuIR. Additionally, the CuIR database enables searches for syntenic genes, Pan-genome data, CRISPR guide sequences, m6A genes, orthologous and paralogous genes, transcription factors, and several important functional genes. To facilitate systematic analysis of Cucurbitaceae plants, the CuIR database includes tools such as Blast, Hmmsearch, Synteny, Primer Design, Jbrowse and Sequence Alignment. The database is continuously updated and improved as new genome data becomes available.

V. viniferaM. charantiaH. pedunculosumS. eduleT. anguinaL. cylindricaL. acutangulaB. hispidaC. metuliferusC. meloC. sativusC. hystrixC. lanatusL. sicerariaC. maximaC. pepoC. argyrospermaC. moschataC. naudinianusC. colocynthisC. rehmiiC. amarusC. ecirrhosusC. mucosospermusS. grosvenorii 4342/18147 647/16231 1249/15985 1035/4501 1275/3077 1210/1867234/515 6/512 1153/3213 6542/9692 2504/3515 911/2524 693/2448 636/1260 107/1094 1003/2883 75/699 371/2306 66/4984 1049/7063 954/5200 697/4076 520/4662 605/3999 406/2213 310/1010 315/1418 139/1180 68/17380/00/0 193/748 227/982 61/3531 315/2804 30/2161 5997/1293 946/1020 86/3001 1369/2393 2338/1628 927/960 51/390 1178/5055 33/10848 180/376 49/63 170/25100255075100125116.0966.73[59.53,73.52]55.23[46.97,61.27][2.64,4.02]3.375.08[4.14,5.86][5.33,7.27]6.4534.41[32.62,36.06][16.29,22.73]20.548.3[6.88,9.67][2.29,3.77]2.976.21[5.02,7.48][19.15,24.79]23.0420.81[17.37,22.44][11.36,15.31]13.537.58[6.27,8.76][5.73,8.01]6.9[5.23,7.34]6.264.59[3.7,5.4]1.31[0.96,1.71][37.1,40.94]39[35.98,38.63]37.36[34.01,35.01]34.5328.57[25.97,31.03][7.82,24.06]13.59Genome familiesExpansion/Contraction WGDWGTMillion years agoNeogenePalaeogeneCretaceousMRCANeogenePalaeogeneCretaceous32911
C u c u r b i t a c e a e I n f o r m a t i on R e s o u r c e ( C u I R ) H e l p T o o l s D a t a b a s e ma nu a l S y n te ny B l a s t P r i m e r d e s i g n H mme a r c h P ro te i n s e qu e n c e s N u c l e i c a c i d s e qu e n c e s R e s o u r c e s S p ec i e s i nfor m at i on D a ta b a s e Chro m o s o m e l e v e l S p ec i e s f i g ur e s G e no me i nfor m at i on R e f e r e n c e s D a ta do w n l o a d d at a b a s e C o n t a c t A ddr e s s Ema i l B r o w s e F un c t i on a l g e n e s G e n e a nno t a t i ons P h y t ohor m on e s F l o w e r i n g g e n e s R e s i s te n c e g e n e s A n t ho c y a n i n g e n e s T r a n s c r i p t i on f a ct or s ( T F ) T F f am i l y c h a rt T F i nfor m at i on N 6- m e t h y l a d e no s i n e ( m 6 A ) P f a m do ma i n S w i s s - P ort T r E M BL N r G e n e O n t o l o g y D e s c r i p t i on CR I S P R G u i d e s e qu e n c e s D up l i c at i on t y pe H o m o l o g s O r t ho l o g s i nfor m at i on O r t ho l o g s t r e e S y n te ny S p ec i e s i n t rodu c t i on d at a b a s e S e a r c h G e no me s y n te ny D o t p l ot B l o c k s G e no m e d at a S p e c i e s i nfor m at i on S ub m i t s p e c i e s G e n e b l o c k s c i r c os R et e n t i on l i n e c h a rt P hone C h a r t s D o t p l ot B l o c k s G e no m e GF F P ro t e i n Do w n l o a d C D S A nno tat i on S i m p l i f y G F F H o m e N e w s V i s i t s T i m e t r e e K s c ur v e c h a rt K a r y o t y p e e v o l u t i on J bro w s e S e qu e n ce a l i g n m e nt E x p a n s i on / Con t r a c t i on P a n - G e n o m e G e n e c l u s te r M e l on W at e r me l on Cu c u m b e r S t ru c t ur a l v a r i a t i ons M et h y l a t i on 5- m e t h y l a d e no s i ne H i s t on e H 3 A n a l y s i s met hods S y n te n y a nd r e a rr a n g em e n t s M e l on W at e r me l on Cu c u m b e r M e l on W at e r me l on Cu c u m b e r F un c t i on a l g e n e s & m 6A T r a n s c r i p t i on f a c t ors A nno tat i ons R N A - s e q E x pr e s s i on h e a t m a p Cu c urb i ta c i n Cu c urb i ta c i n s y n t h e s i s g e n e s H e te ro l o g ou s b i o s y n t h e s i s of Cu c urb i ta d i e nd

Project Timeline

1. Project start: July 2023

2. Data collection and analysis: August 2023

3. Build Home: November 2023

4. Build Browse: January 2024

5. Build Pan-genome: April 2024

6. Build Search: July 2024

7. Build Tools: August 2024

8. Build Others: October 2024

9. Website online: November 2024

10. Add Pan-genome: February 2025

11. Add Jbrowse and Sequence Alignment tools: April 2025

12. Add species display page: June 2025






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