Comparative genomics reveal the remarkable conservation of gene order in these two plant species for over 300 million years.
A recent study was published in PNAS (the Proceedings of National Academy of Sciences) on January 18 of this year, and it sought to compare the genomes of two plants, Huperzia asiatica and Diphasiastrum complanatum, which diverged some 350 million years ago. They hoped this would help us learn more about the nature of their evolution and how they differ from other groups of plants.
But before we get into the details, it might help to define some keywords used in the paper. (If you want to skip to the summary, click here.)
Keywords
Lycophyte
The oldest lineage of extant vascular plants (plants containing xylem and phloem tissues for transport of water, minerals and products of photosynthesis). In a phylogenetic perspective, the lycophytes would be the sister group to all other vascular plants.
The lycophytes include plants such as clubmosses, firmosses and quillworts. They may look like moss but mosses are non-vascular whereas lycophytes are vascular.
Lycophytes reproduce by spores and can either by homosporous or heterosporous.
Homosporous
Describes plants that produce only one type of spore. The spore develops into a plant form called a gametophyte, which produces both the sperm and egg cells that will go on to produce the next generation.
Homosporous lycophytes have a larger genome size and more chromosomes than heterosporous lycophytes.
Heterosporous
Describes plants that produce two types of spores. The spores develop into distinct gametophytes, each producing either sperm (male gametophytes) or egg cells (female gametophytes).
Synteny
In traditional genetics, synteny simply describes genes that are found on the same chromosome.
In current genetics, synteny is synonymous with collinearity, meaning the conservation of gene order across species.
Syntenic genes are often grouped in syntenic blocks — the gene order within the blocks shared by two species is the same as the order in their most recent common ancestor.
Whole genome duplication (WGD) events
Events in which the entire genome of a species doubled, often as a result of errors during meiosis.
Club moss growing from ground covered with decayed leaves. (Source | License)
A new discovery in plant evolution
Heterosporous and homosporous lycophytes have diverged from a common ancestor around 400 million years ago (mya). However, Li and his team noted that there was limited information and research on the homosporous genomes. He therefore made it his goal to analyse, assemble and compare the genomes of two homosporous lycophytes, Huperzia asiatica and Diphasiastrum complanatum, hoping to shed some light onto how the two lycophyte groups truly differ on the genomic level.
What they found was remarkable, to say the least. About 30% of the two lycophytes’ genes remained in syntenic blocks — they are organised in the same order with respect to each other — despite the 350 million years that had passed since they diverged from each other.
Moreover, Li et al. identified individual WGD events that occurred to each of the two species. Usually, these would have led to major structural changes to their genomes. Although some duplicate genes may evolve new functions and remain in the genome, most will be lost due to a lack of selective pressure acting on them, also known as redundancy — they had no reason to be there if they served the same function as the original copy.
These findings go against the general understanding of large-scale genome reorganisations that occurs after WGD events, and the researchers still aren’t sure why the genomes of H. asiatica and D. complanatum exhibit such levels of conservation. They believe further studies on homosporous plants can help answer a wide range of questions surrounding not just plant genetics, but also the evolution of land vascular plants.
References:
Boyce Thompson Institute. A window into plant evolution: The unusual genetic journey of lycophytes [Internet]. 2024. ScienceDaily. Available from: www.sciencedaily.com/releases/2024/01/240118150803.htm.
Li C, et al. Extraordinary preservation of gene collinearity over three hundred million years revealed in homosporous lycophytes. PNAS, 2024, Jan, 18;121(4):e2312607121.
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