PUBLICATION

Co-first and co-corresponding author papers

1. Jiao C#, Sørensen I#, Sun X#, Sun H, Behar H, Alseekh S, Philippe G, Lopez KP, Sun L, Reed R, Jeon S, Kiyonami R, Zhang S, Fernie AR, Brumer H, Domozych DS, Fei Z, Rose JKC. The Penium margaritaceum genome: hallmarks of the origins of land plants. Cell 181: 1097-1111.e1012.

2. Xu C#, Jiao C#*, Sun H#, Cai X, Wang X, Ge C, Zheng Y, Liu W, Sun X, Xu Y, Deng J, Zhang Z, Huang S, Dai S, Mou B, Wang Q, Fei Z*, Wang Q*. 2017. Draft genome of spinach and transcriptome diversity of 120 Spinacia accessions. Nature Communications 8: 15275.

3. Sun X#, Jiao C#, Schwaninger H#, Chao T, Ma Y, Duan N, Khan A, Ban S, Xu K, Cheng L, Zhong GY, Fei Z. Phased diploid genome assemblies and pan-genomes unravel genetic basis of apple domestication. Nature Genetics 52: 1423-1432.

4. Jiao C, Gao M, Wang X, Fei Z. 2015. Transcriptome characterization of three wild Chinese Vitis uncovers a large number of distinct disease related genes. BMC Genomics 16: 223.

5. Wei Q#, Jiao C#, Guo L, Ding Y, Cao J, Feng J, Dong X, Mao L, Sun H, Yu F, Yang G, Shi P, Ren G, Fei Z. 2017. Exploring key cellular processes and candidate genes regulating the primary thickening growth of Moso underground shoots. New Phytologist 214: 81-96.

6. Wei Q#, Guo L#, Jiao C#, Fei Z, Chen M, Cao J, Ding Y, Yuan Q. 2019. Characterization of the developmental dynamics of the elongation of a bamboo internode during the fast growth stage. Tree physiology 39: 1201-1214.

7. Wei Q#, Jiao C#, Ding Y, Gao S, Guo L, Chen M, Hu P, Xia S, Ren G, Fei Z. 2018. Cellular and molecular characterizations of a slow-growth variant provide insights into the fast growth of bamboo. Tree physiology 38: 641-654.

8. Piedra-Aguilera A#, Jiao C#, Luna AP, Villanueva F, Dabad M, Esteve-Codina A, Diaz-Pendon JA, Fei Z, Bejarano ER, Castillo AG. 2019. Integrated single-base resolution maps of transcriptome, sRNAome and methylome of Tomato yellow leaf curl virus (TYLCV) in tomato. Scientific reports 9: 2863.

9. Xu C#, Jiao C#, Zheng Y, Sun H, Liu W, Cai X, Wang X, Liu S, Xu Y, Mou B, Dai S, Fei Z, Wang Q. 2015. De novo and comparative transcriptome analysis of cultivated and wild spinach. Scientific reports 5: 17706.

10. Cai X, Jiao C*, Sun H, Wang X, Xu C, Fei Z, Wang Q*. 2017. The complete mitochondrial genome sequence of spinach, Spinacia oleracea L. Mitochondrial DNA Part B 2: 339-340.

Co-author papers

1. Philippe G, Sorensen I, Jiao C, Sun X, Fei Z, Domozych DS, Rose JK. 2020. Cutin and suberin: assembly and origins of specialized lipidic cell wall scaffolds. Current Opinion in Plant Biology 55: 11-20.

2. Wang X, Gao L, Jiao C, Stravoravdis S, Hosmani P, Saha S, Zhang J, Mainiero S, Strickler S, Catala C, Martin G, Mueller L, Vrebalov J, Giovannoni J, Wu S, Fei Z. 2020. Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding. Nature communications. 11: 5817.

3. Domozych DS, Sun L, Palacio-Lopez K, Reed R, Jeon S, Li M, Jiao C, Sorensen I, Fei Z, Rose JKC. 2020. Endomembrane architecture and dynamics during secretion of the extracellular matrix of the unicellular charophyte, Penium margaritaceum. Journal of experimental botany doi:10.1093/jxb/eraa039.

4. Montrose DC, Nishiguchi R, Basu S, Staab HA, Zhou XK, Wang H, Meng L, Johncilla M, Cubillos-Ruiz JR, Morales DK, Wells MT, Simpson KW, Zhang S, Dogan B, Jiao C, Fei Z, Oka A, Herzog JW, Sartor RB, Dannenberg AJ. Dietary fructose alters the composition, localization and metabolism of gut microbiota in association with worsening colitis. Cellular and Molecular Gastroenterology and Hepatology doi:10.1016/j.jcmgh.2020.09.008.

5. Wang L, Zhang S, Jiao C, Li Z, Liu C, Wang X. QTL-seq analysis of seed size trait in grape reveal new insight on the genetics of seedlessness. Under review.

6. Gao M, Wan R, Zhu Y, Jiao C, Cheng C, Fei Z, Wang X. Comparative transcriptome analysis of leaves from two grapevine species reveals an early gene expression profile associated with Elsinoe ampelina resistance. Under review.

7. Wan R, Hou X, Gao M, Zhang S, Jiao C,  Wang M, Guo R, Li Z, Fei Z, Wang X.  Comparative transcriptomics reveal contrasting levels of resistances of Vitis vinifera and Chinese Wild Vitis amurensis to Botrytis cinerea. Under review.

8. Zheng Y, Wu S, Bai Y, Sun H, Jiao C, Guo S, Zhao K, Blanca J, Zhang Z, Huang S, Xu Y, Weng Y, Mazourek M, U KR, Ando K, McCreight JD, Schaffer AA, Burger J, Tadmor Y, Katzir N, Tang X, Liu Y, Giovannoni JJ, Ling KS, Wechter WP, Levi A, Garcia-Mas J, Grumet R, Fei Z. 2019. Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops. Nucleic Acids Research 47: D1128-D1136.

9. Guo L, Sun X, Li Z, Wang Y, Fei Z, Jiao C, Feng J, Cui D, Feng X, Ding Y, Zhang C, Wei Q. 2019. Morphological dissection and cellular and transcriptome characterizations of bamboo pith cavity formation reveal a pivotal role of genes related to programmed cell death. Plant biotechnology journal 17: 982-997.

10. Wang Y, Sun X, Ding Y, Fei Z, Jiao C, Fan M, Yao B, Xin P, Chu J, Wei Q. 2019. Cellular and molecular characterization of a thick-walled variant reveal a pivotal role of shoot apical meristem in transverse development of bamboo culm. Journal of experimental botany 70: 3911-3926.

11. Tang W, Sun X, Yue J, Tang X, Jiao C, Yang Y, Niu X, Miao M, Zhang D, Huang S, Shi W, Li M, Fang C, Fei Z, Liu Y. 2019. Chromosome-scale genome assembly of kiwifruit Actinidia eriantha with single-molecule sequencing and chromatin interaction mapping. Gigascience 8.

12. Pan C, Yang D, Zhao X, Jiao C, Yan Y, Lamin‐Samu AT, Wang Q, Xu X, Fei Z, Lu G. 2019. Tomato stigma exsertion induced by high temperature is associated with the jasmonate signalling pathway. Plant, cell & environment 42: 1205-1221.

13. Collins K, Zhao K, Jiao C, Xu C, Cai X, Wang X, Ge C, Dai S, Wang Q, Wang Q, Fei Z, Zheng Y. 2019. SpinachBase: a central portal for spinach genomics. Database 2019.

14. Liu W, Zhang J, Jiao C, Yin X, Fei Z, Wu Q, Chen K. 2019. Transcriptome analysis provides insights into the regulation of metabolic processes during postharvest cold storage of loquat (Eriobotrya japonica) fruit. Horticulture research 6: 1-11.

15. Wu S, Lau KH, Cao Q, Hamilton JP, Sun H, Zhou C, Eserman L, Gemenet DC, Olukolu BA, Wang H, Crisovan E, Godden GT, Jiao C, Wang X, Kitavi M, Manrique-Carpintero N, Vaillancourt B, Wiegert-Rininger K, Yang X, Bao K, Schaff J, Kreuze J, Gruneberg W, Khan A, Ghislain M, Ma D, Jiang J, Mwanga ROM, Leebens-Mack J, Coin LJM, Yencho GC, Buell CR, Fei Z. 2018. Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement. Nature Communications 9: 4580.

16. Galpaz N, Gonda I, Shem-Tov D, Barad O, Tzuri G, Lev S, Fei Z, Xu Y, Mao L, Jiao C, Harel-Beja R, Doron-Faigenboim A, Tzfadia O, Bar E, Meir A, Sa'ar U, Fait A, Halperin E, Kenigswald M, Fallik E, Lombardi N, Kol G, Ronen G, Burger Y, Gur A, Tadmor Y, Portnoy V, Schaffer AA, Lewinsohn E, Giovannoni JJ, Katzir N. 2018. Deciphering genetic factors that determine melon fruit-quality traits using RNA-Seq-based high-resolution QTL and eQTL mapping. The Plant Journal 94: 169-191.

17. Wang X, Bao K, Reddy UK, Bai Y, Hammar SA, Jiao C, Wehner TC, Ramirez-Madera AO, Weng Y, Grumet R, Fei Z. 2018. The USDA cucumber (Cucumis sativus L.) collection: genetic diversity, population structure, genome-wide association studies, and core collection development. Horticulture research 5: 64.

18. Duan N, Bai Y, Sun H, Wang N, Ma Y, Li M, Wang X, Jiao C, Legall N, Mao L, Wan S, Wang K, He T, Feng S, Zhang Z, Mao Z, Shen X, Chen X, Jiang Y, Wu S, Yin C, Ge S, Yang L, Jiang S, Xu H, Liu J, Wang D, Qu C, Wang Y, Zuo W, Xiang L, Liu C, Zhang D, Gao Y, Xu Y, Xu K, Chao T, Fazio G, Shu H, Zhong GY, Cheng L, Fei Z, Chen X. 2017. Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement. Nature Communications 8: 249.

19. Sun H, Wu S, Zhang G, Jiao C, Guo S, Ren Y, Zhang J, Zhang H, Gong G, Jia Z, Zhang F, Tian J, Lucas WJ, Doyle JJ, Li H, Fei Z, Xu Y. 2017. Karyotype stability and unbiased fractionation in the paleo-allotetraploid Cucurbita genomes. Molecular plant 10: 1293-1306.

20. Yan J, Chia JC, Sheng H, Jung HI, Zavodna TO, Zhang L, Huang R, Jiao C, Craft EJ, Fei Z, Kochian LV, Vatamaniuk OK. 2017. Arabidopsis pollen fertility requires the transcription factors CITF1 and SPL7 that regulate copper delivery to anthers and jasmonic acid synthesis. The Plant Cell 29: 3012-3029.

21. Xu C, Sun X, Taylor A, Jiao C, Xu Y, Cai X, Wang X, Ge C, Pan G, Wang Q, Fei Z, Wang Q. 2017. Diversity, distribution, and evolution of tomato viruses in China uncovered by small RNA sequencing. Journal of virology 91: e00173-00117.

22. Tafolla-Arellano JC, Zheng Y, Sun H, Jiao C, Ruiz-May E, Hernandez-Onate MA, Gonzalez-Leon A, Baez-Sanudo R, Fei Z, Domozych D, Rose JKC, Tiznado-Hernandez ME. 2017. Transcriptome analysis of mango (Mangifera indica L.) fruit epidermal peel to identify putative cuticle-associated genes. Scientific reports 7: 46163.

23. Zhang B, Tieman DM, Jiao C, Xu Y, Chen K, Fei Z, Giovannoni JJ, Klee HJ. 2016. Chilling-induced tomato flavor loss is associated with altered volatile synthesis and transient changes in DNA methylation. Proceedings of the National Academy of Sciences 113: 12580-12585.

24. Zheng Y, Jiao C, Sun H, Rosli HG, Pombo MA, Zhang P, Banf M, Dai X, Martin GB, Giovannoni JJ, Zhao PX, Rhee SY, Fei Z. 2016. iTAK: A program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators, and protein kinases. Molecular plant 9: 1667-1670.

25. Wang L, Hu X, Jiao C, Li Z, Fei Z, Yan X, Liu C, Wang Y, Wang X. 2016. Transcriptome analyses of seed development in grape hybrids reveals a possible mechanism influencing seed size. BMC Genomics 17: 898.

26. Yin X, Singer SD, Qiao H, Liu Y, Jiao C, Wang H, Li Z, Fei Z, Wang Y, Fan C, Wang X. 2016. Insights into the mechanisms underlying ultraviolet-C induced resveratrol metabolism in grapevine (V. amurensis Rupr.) cv. "Tonghua-3". Frontiers in plant science 7: 503.

27. Jing X, White TA, Luan J, Jiao C, Fei Z, Douglas AE. 2016. Evolutionary conservation of candidate osmoregulation genes in plant phloem sap-feeding insects. Insect molecular biology 25: 251-258.

28. Zhang Z, Mao L, Chen H, Bu F, Li G, Sun J, Li S, Sun H, Jiao C, Blakely R, Pan J, Cai R, Luo R, Van de Peer Y, Jacobsen E, Fei Z, Huang S. 2015. Genome-wide mapping of structural variations reveals a copy number variant that determines reproductive morphology in cucumber. The Plant Cell 27: 1595-1604.

29. Cheng C, Jiao C, Singer SD, Gao M, Xu X, Zhou Y, Li Z, Fei Z, Wang Y, Wang X. 2015. Gibberellin-induced changes in the transcriptome of grapevine (Vitis labrusca× V. vinifera) cv. Kyoho flowers. BMC Genomics 16: 128.

30. Yang Y, Mao L, Jittayasothorn Y, Kang Y, Jiao C, Fei Z, Zhong G-Y. 2015. Messenger RNA exchange between scions and rootstocks in grafted grapevines. BMC plant biology 15: 251.

31. Guo S, Sun H, Zhang H, Liu J, Ren Y, Gong G, Jiao C, Zheng Y, Yang W, Fei Z, Xu Y. 2015. Comparative transcriptome analysis of cultivated and wild watermelon during fruit development. PLoS one 10: e0130267.

32. Hou HM, Li HE, Gao M, Wang H, Jiao C, Wang XP. 2013. Expression of a GDP-L-galactose phosphorylase-like gene in a Chinese wild Vitis species induces responses to Erysiphe necator and defense signaling molecules. Genetics and Molecular Research 12: 3830-3844.

33. Wen Z, Gao M, Jiao C, Wang Q, Xu H, Walter M, Xu W, Bassett C, Wang X. 2012. Characterization and expression analysis of a retinoblastoma-related gene from Chinese wild Vitis pseudoreticulata. Plant molecular biology reporter 30: 983-991.

34. Gao M, Niu J, Zhao S, Jiao C, Xu W, Fei Z, Wang X. 2012. Characterization of Erysiphe necator-responsive genes in Chinese wild Vitis quinquangularis. International journal of molecular sciences 13: 11497-11519.

35. Wang Q, Zhang Y, Gao M, Jiao C, Wang X. 2011. Identification and expression analysis of a pathogen-responsive PR-1 gene from Chinese wild Vitis quinquangularis. African Journal of Biotechnology 10: 17062-17069.