Comprehensive isoform-level analysis reveals the contribution of alternative isoforms to venom evolution and repertoire diversity
- Xinhai Ye1,2,3,
- Chun He1,
- Yi Yang1,
- Yu H. Sun4,
- Shijiao Xiong1,
- Kevin C. Chan2,
- Yuxuan Si3,
- Shan Xiao1,
- Xianxin Zhao1,
- Haiwei Lin1,
- Yang Mei1,
- Yufeng Yao5,
- Gongyin Ye1,
- Fei Wu2,3 and
- Qi Fang1
- 1State Key Laboratory of Rice Biology and Breeding & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China;
- 2Shanghai Institute for Advanced Study, Zhejiang University, Shanghai 201203, China;
- 3College of Computer Science and Technology, Zhejiang University, Hangzhou 310027, China;
- 4Department of Biology, University of Rochester, Rochester, New York 14627, USA;
- 5Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310020, China
Abstract
Animal venom systems have emerged as valuable models for investigating how novel polygenic phenotypes may arise from gene evolution by varying molecular mechanisms. However, a significant portion of venom genes produce alternative mRNA isoforms that have not been extensively characterized, hindering a comprehensive understanding of venom biology. In this study, we present a full-length isoform-level profiling workflow integrating multiple RNA sequencing technologies, allowing us to reconstruct a high-resolution transcriptome landscape of venom genes in the parasitoid wasp Pteromalus puparum. Our findings demonstrate that more than half of the venom genes generate multiple isoforms within the venom gland. Through mass spectrometry analysis, we confirm that alternative splicing contributes to the diversity of venom proteins, acting as a mechanism for expanding the venom repertoire. Notably, we identified seven venom genes that exhibit distinct isoform usages between the venom gland and other tissues. Furthermore, evolutionary analyses of venom serpin3 and orcokinin further reveal that the co-option of an ancient isoform and a newly evolved isoform, respectively, contributes to venom recruitment, providing valuable insights into the genetic mechanisms driving venom evolution in parasitoid wasps. Overall, our study presents a comprehensive investigation of venom genes at the isoform level, significantly advancing our understanding of alternative isoforms in venom diversity and evolution and setting the stage for further in-depth research on venoms.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.277707.123.
- Received January 16, 2023.
- Accepted August 8, 2023.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see https://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.