Lygodium microphyllum v1.1.9 genome assembly and annotation

Lygodium microphyllum is a highly invasive vining fern. Here, we present the sequencing, assembly, and analysis of the Lygodium microphyllum genome including transcriptomic and epigenomic variation between the gametophyte and sporophyte life phases.

In this repository, we include the assembly and annotation files for the Lygodium microphyllum v1.1.9 genome. 

This data is published in the article: 

The genome of the vining fern Lygodium microphyllum highlights genomic and functional differences between life phases of an invasive plant. Proceedings of the National Academy of Sciences 122(39): e2504773122. https://doi.org/10.1073/pnas.2504773122

Publication Abstract: 

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.

Sequence data have been deposited in NCBI SRA under BioProject PRJNA1157352 and from 10KP at https://db.cngb.org/search/organism/148566/. The genome assembly is available at NCBI under Accession JBLQGR000000000. Genome assembly and annotations are also available at FernBase (https://fernbase.org/). All code used in this study is available at https://github.com/jessiepelosi/LygodiumGenome.