Husna, Amity University Kolkata
What are Ferns and why are they unique?
Ferns (Polypodiopsida) are a group of vascular plants and are considered to be the most diversified group of land plants after angiosperms. They occupy a wide range of habitats including grasslands, forests, deserts, mountainous regions, and aquatic environments. Due to their huge diversification, they contribute significantly to ecosystem functioning by serving as a habitat for invertebrates, shaping the recolonization of plants from disturbed habitats and also influence the composition of tree species communities. Despite being so important, most taxa of ferns are very poorly covered by genomic resources and the data based on high-resolution markers of species studies are entirely lacking.
Why is the transcriptome-wide study of ferns needed?
Most of the ferns have two independent stages of life cycles, namely, the gametophytic and sporophytic stages. This flexibility in the reproductive system has contributed to the evolution of fern lifestyles and their diversification. Ferns have been estimated to be ca. 360–431 million years old, this explains the deep divergence among ferns lineages. The phylogenetic analysis of ferns has been mostly established based on chloroplast markers, sometimes combined either with mitochondrial or nuclear markers. But the heavy dependence on these markers largely prevents analyses of reticulation events including hybridization and introgression. Moreover, recent phylogenetic studies have highlighted the potentiality of transcriptome-based approaches. In order to overcome challenges imposed by high degrees of paralogy in various fern genomes, it’s very essential to obtain the transcriptome-wide datasets of expanding genomes.
Recent 2021 study
A recent study by researchers, published on Molecular Ecology Resources was performed on the genus Botrychium which belongs to the family Ophioglossaceae. It includes species with very large genomes and chromosome numbers (For instance, Ophioglossum reticulatum 2n = 1,520). The genus has a varied multiracial distribution with 35 species, half of which are polyploids. Botrychium lunaria (L.) Sw. is a diploid species with an extremely large genome of about ~19.0–23.7 Gb.
Methodology adopted
- The researchers established a transcriptome for Botrychium lunaria (L.) Sw. By deep RNA sequencing of a single individual, they gathered 25,677 high-quality transcripts with an average length of 1,333 bp.
- Then, the researchers sequenced eleven additional transcriptomes of individuals from two populations (intraspecies) in Switzerland that included the population of the reference individual. 374,463 single nucleotide polymorphisms (SNPs) were identified based on read mapping and were segregated among individuals for an average density of 14 SNPs per kilobase. High-quality transcriptomic resources and SNP sets account for a very powerful population of genomic resources which would help to easily find out the diverse ecology, and evolution of fern populations.
- They even constructed a phylogenomic tree of 92 taxa that represented all fern orders. This was done to find out the positioning of the genus Botrychium.
Significance of the study
Transcriptome-wide SNPs have enabled a fine-grained analysis of demographic history which would help to investigate the consequences of the complex mating systems and putative polyploidization events. Moreover, ecological genomics studies that are based on transcriptomic markers will provide the first opportunities to anatomize adaptation to the local environment within fern species. It was found that the 12 transcriptomes were most likely from diploid individuals. Hence, the transcriptome-wide markers have provided a striking resolution of the population genetic structure, and it has revealed the considerable variation in heterozygosity among individuals.
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Reference: Mossion, V., Dauphin, B., Grant, J., Kessler, M., Zemp, N., & Croll, D. (2021). Transcriptome‐wide SNPs for Botrychium lunaria ferns enable fine‐grained analysis of ploidy and population structure. Molecular Ecology Resources, 1755-0998.13478. https://doi.org/10.1111/1755-0998.13478
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About the Author
Husna is an undergraduate student of BTech Biotechnology at Amity University Kolkata. She is a research enthusiast in Immunology and Immunotherapy. However, she has a keen interest in various other Bioscience subjects as well. Husna is constantly focused on improving her knowledge and laboratory skills through various internships. She is a Scientific content writer who has knowledge in diverse backgrounds of Biotechnology.
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