Dr. Ai Kitazumi, Ph.D.
Plant and Soil Science
Email: ai.kitazumi@ttu.edu
I have been working for Dr. de los Reyes since undergraduate (genotyping overexpression
lines, making transformation constructs), master's (cis element analysis in orthologous
transcription factors, miRNA profiling and target prediction in landraces of potatoes,
comparative genomics of wild species of Oryza), Ph.D (high throughput sequencing on salinity tolerant individuals in transgressive
rice population), moving from wet lab experiments to bioinformatics.
In our projects on stress response in rice and cotton, my function is a rice genome/transcript
assembler with a goal to understand a mechanism of how genome shock upon hybridization
of genetically distant parents and through successive rounds of meiosis, through integrating
DNA-seq, RNA-seq, BS-seq, and action of ncRNA and transposons.
Current analysis have revealed variation beyond SNP level and I am working on further
analysis that might change how we look at hybrids and breeding lines.
Key Skills
Expression analysis and network prediction from mRNA-seq and sRNA-seq, de novo assembly and structural variation detection from DNA-seq, methylome/RdDM analysis, transposable element and long ncRNA profiling
Publications
- Kitazumi A, Pabuayon ICM, Ohyanagi H, Fujita M, Osti B, Shenton MR, Kakei Y, Nakamura Y, Brar DS, Kurata N, De los Reyes BG (2018). Potential of Oryza officinalis to augment the cold tolerance genetic mechanisms of Oryza sativa by network complementation. Nature Scientific Reports 8:16346.
- De los Reyes BG, Kim YS, Mohanty B, Kumar A, Kitazumi A, Pabuayon ICM, Sandhu N, Lee DY (2017) Cold and water deficit regulatory mechanisms in rice – Optimizing stress tolerance potential by pathway integration and network engineering. In ‘Rice Genomics, Genetics, and Breeding', T. Sasaki and M. Ashikari (Eds.), Springer-Nature Publishing, DOI:978-981-10-7460-8.
- Alpuerto JB, Mukherjee A, Kitazumi A, Alyokhin A, De Koeyer D, De los Reyes BG (2017) Impaired expressions of the beta and delta isoforms of vacuolar processing enzymes compromise the basal defenses of Arabidopsis thaliana against the phloem-feeding insect Myzus persicae. Acta Physiologia Plantarum 39:e233.
- Panes VA, Kitazumi A, Butler M, Baoas A, De los Reyes BG (2017) Analysis of the oil biosynthesis transcripts of the Moringa oleifera Lam. mature seed embryos using RNA sequencing. Acta Horticulturae 1158: 55-62. DOI 10.17660/ActaHortic.2017.1158.7.
- Mohanty B, Kitazumi A, Cheung CYM, Lakshmanan M, De los Reyes BG, Jang IC, Lee DY (2016) Identification of candidate network hubs involved in metabolic adjustments of rice under drought stress by integrating transcriptome data and genome-scale metabolic network. Plant Science, 242:224–239.
- Chen J, Kitazumi A, Alpuerto J, Alyokhin A, De los reyes B. Heat-induced mortality and expression of heat shock proteins in Colorado potato beetles treated with imidacloprid. Insect Sci. 2016;23(4):548-54.
- Kitazumi A, Kawahara Y, Onda TS, De Koeyer D, de los Reyes BG (2015) Implications of miR166 and miR159 induction to the basal response mechanisms of an andigena potato (Solanum tuberosum subsp. andigena) to salinity stress, predicted from network models in Arabidopsis. Genome 58(1): 13-24. [Highly accessed]
- Xu F, Park MR, Kitazumi A, Herath V, Mohanty B, Yun SJ, De los Reyes BG (2012) Cis-regulatory signatures among orthologous groups of stress-associated bZIP transcription factors from rice, sorghum and Arabidopsis based on phylogenetic footprints. BMC Genomics 13:e497.
Additional Info
Department of Plant and Soil Science
-
Address
Texas Tech University, Department of Plant and Soil Science, Box 42122, Lubbock, TX 79409 -
Phone
806.742.2838 -
Email
psstechsupport@ttu.edu