The genome of the vining fern Lygodium microphyllum highlights genomic and functional differences between life phases of an invasive plant

• 成果类型: Article
• 署名作者: Pelosi, Jessie A.; Davenport, Ruth; Kuo, Li- Yaung; Gray, Levi N.; Dant, Anthony J.; Kim, Emily H.; Li, Fay - Wei; Dlugosch, Katrina M.; Krabbenhoft, Trevor J.; Barbazuk, William Bradley; Sessa, Emily B.
• 署名单位: State University System of Florida; University of Florida; University of Arizona; National Tsing Hua University; State University of New York (SUNY) System; University at Buffalo, SUNY; State University System of Florida; University of Florida; Cornell University; Boyce Thompson Institute for Plant Research; Cornell University; State University System of Florida; University of Florida; New York Botanical Garden
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-9161
• DOI: 10.1073/pnas.2504773122
• 发表日期: 2025-09-30
• 关键词: evolutionary consequences; intron retention; genes; tolerance; gametophytes; sex; sporophytes; insights; provides; maltose

摘要

Functional and genomic studies on the differences between the gametophyte and sporophyte life phases of plants remain scarce, yet unraveling these dynamics is crucial to understanding the biology of plants and the success of each phase under different conditions. Here, we provide a reference genome for the highly invasive fern Lygodium microphyllum and compare the transcriptomic and epigenomic landscapes of its gametophyte and sporophyte life phases. Under ambient conditions, we found differential regulation and splicing of developmental genes (homeobox and MADS-box clades) may play a role in the genomic determination of the haploid and diploid life stages. We generated a base pair-resolution methylome of a fern gametophyte, and determined that methylation patterns are remarkably similar between vegetative tissues despite their morphological and functional differences. We further explored the physiological and transcriptomic responses of gametophytes and sporophytes to freezing stress, the most likely abiotic factor limiting further range expansion of this invasive species. While controlled by the same genome, we show that life phases and tissues use alternative molecular pathways in response to freezing and greater physiological resilience in the gametophyte life stage to this stressor. Our results underscore the need to incorporate both life phases when developing effective mitigation strategies, as differential responses to environmental stressors between phases reveal opportunities for management approaches (e.g., targeting gametophytes in addition to sporophytes). These genomic resources fill a gap in our understanding of fundamental plant biology and inform invasive species research.