Dr. Xiangjia “Jack” Min, Associate Professor in Biological Science, published a research article in Computational Molecular Biology in September 2017.
Title: Comprehensive Cataloging and Analysis of Alternative Splicing in Maize
Author: Dr. Xiangjia “Jack” Min
Gene expression is a key step in developmental regulation and responses in changing environments in plants. Alternative splicing (AS) is a process generating multiple RNA isoforms from a single gene pre-mRNA transcript that increases the diversity of functional proteins and RNAs. Identification and analysis of alternatively splicing events are critical for crop improvement and understanding regulatory mechanisms. In maize large numbers of transcripts generated by RNA-seq technology are available, we incorporated these data with data assembled with ESTs and mRNAs to comprehensively catalog all genes undergoing AS. A total of 192,624 AS events were detected and classified, including 103,566 (53.8%) basic events and 89,058 (46.2%) complex events which were formed by combination of various types of basic events. Intron retention was the dominant type of basic AS event, accounting for 24.1%. These AS events were identified from 91,128 transcripts which were generated from 26,669 genomic loci, of which consisted of 20,860 gene models. It was estimated that 55.3% maize genes may be subjected to AS. The transcripts mapping information can be used to improve the predicted gene models in maize. The data can be accessed at Plant Alternative Splicing Database (http://proteomics.ysu.edu/altsplice/).
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Dr. Xiangjia “Jack” Min, Associate Professor in Biological Science, in collaboration with Dr. Feng Yu, Assistant Professor in Computer Science and Information Systems published a research article in Current Plant Biology in July 2017.
Title: “Comparative landscape of alternative splicing in fruit plants”
Authors: G Sablok, B Powell, J Braessler, F Yu F, XJ Min
Alternative splicing (AS) has played a major role in defining the protein diversity, which could be linked to phenotypic alternations. It is imperative to have a comparative resolution of AS to understand the pre-mRNAs splicing diversity. In the present research, we present a comparative assessment of the AS events in four different fruit plants including apple (Malus domestica), grape (Vitis vinifera), sweet orange (Citrus sinensis), and woodland strawberry (Fragaria vesca), using spliced mapping of the expressed sequence tags and mRNA sequences. We identified a total of 2039 AS events in apple, 2454 in grape, 1425 in orange, and 631 in strawberry, respectively. In this study grape displayed the maximum number of genes (1588) associated with the splicing, followed by apple (1580), orange (1133) and strawberry (444). Transcripts mapping analysis shows that grape plant has relatively larger intron sizes than introns in other fruit species. The data provide a basis for further functional characterization of the genes undergoing AS and can be accessed at Plant Alternative Splicing Database (http://proteomics.ysu.edu/altsplice/plant/).
Full article link: http://www.sciencedirect.com/science/article/pii/S2214662817300439