1. Supplementary Materials of Article A long-read transcriptome assembly of cotton (Gossypium hirsutum) and intraspecific SNP discovery Hamid Ashrafi 1 *, Amanda M. Hulse-Kemp 2, Fei Wang 2, Joshua Udall 3, Don Jones 4, Marta Matvienko 5, Keithanne Mockaitis 6, David M. Stelly 2, Allen Van Deynze 1 1- University of California-Davis, Department of Plant Sciences and Seed Biotechnology Center, One Shields Ave, Davis CA 95616 2- Texas A&M University, Department of Soil and Crop Sciences, College Station, TX 77843 3- Brigham Young University, Plant and Wildlife Science Department, Provo, UT 84062 4- Cotton Incorporated, Cary, NC 27513 5- University of California-Davis, Genome Center, One Shields Ave, Davis CA 95616 Current Address: CLC bio, Cambridge, Massachusetts, United States of America 6- Department of Biology, Indiana University, 915 E. Third St., Bloomington IN 47405

2. Fig. S1 N50=1100 Max = 13,697 Min = 101

3. Fig. S2

4. Fig. S3

5. Fig. S4

6. Fig. S5

7. Fig. S6

8. Fig. S7

9. Fig. S8

10. Fig. S9

11. Fig. S10

12. Fig. S11

13. Chr 1 Fig. S12-a. Alignment of TM-1 454 and EST sequences to the genome of G. raimondii. a-d) alignment of G. raimondii genes, CDS, Gene based expression and translated region expression to its own genome sequence, respectively. e), f) depicts the left and right had side of break points when TM-1 Reads mapped to G. raimondii genome. g) large InDels h) structural variants. abcdefghabcdefgh

14. Chr 2 Fig. S12-b

15. Chr 3 Fig. S12-c

16. Chr 4 Fig. S12-d

17. Chr 5 Fig. S12-e

18. Chr 6 Fig. S12-f

19. Chr 7 Fig. S12-g

20. Chr 8 Fig. S12-h

21. Chr 9 Fig. S12-i

22. Chr 10 Fig. S12-j

23. Chr 11 Fig. S12-k

24. Chr 12 Fig. S12-l

25. Chr 13 Fig. S12-m