They joy of genome sequencing: when genomics meets natural history

When I have a massive pile of papers that I need to read, I can’t help but look at the ones with interesting natural history first. There’s something exceptionally satisfying about using modern tools to dig deeper into the features that make each species so interesting. Many molecular ecologists, myself included, started a career in biology because of a love of natural history, and I think it’s great when this passion can be captured in modern research. One area where an understanding of an organism’s natural history is perhaps surprisingly important is in whole genome sequencing. While it’s becoming increasingly common to sequence, assemble and annotate genomes (though I’d still argue it’s challenging to do it well), many papers do more than just generate a genomic resource, and relate genomic variants to unique properties of a species. Even better is when these interesting features of a species can be related to other experimental work, or sequencing additional natural populations, to gain deeper insights into organismal biology.

The pitcher plant Cephalotus follicularis (picture H. Zell for Wikipedia)

One example is the paper that describes the genome of the carnivorous pitcher plant Cephalotus (Fukushima et al. 2017). Carnivorous plants have evolved on multiple occasions and use a sophisticated range of traps to attract, catch and digest prey in nutrient-poor environments. The highlight of the paper is that the authors manage to induce the switch between pitcher trap and flat leaf by changing ambient temperature, and then use transcriptomic comparisons to pinpoint differentially expressed genes involved in leaf development. This neat trick reveals a number of candidate genes involved in pitcher formation, including AS2, YAB5, and WOX1 orthologues. They also looked at the digestive proteins in Cephalotus and other taxa representing independent origins of carnivory, and find shared proteins that are repeatedly co-opted in the evolution of this novel phenotype. I came away from reading the paper being even more intrigued about how these amazing plants have evolved, and thinking that there’s so much we can now address with careful genomic and transcriptomic analyses.

And who can forget the passenger pigeon genome papers? The passenger pigeon (Ectopistes migratorius) was at one point perhaps the most abundant bird species on earth, with a census population size in the billions, before its unprecedented extinction in the 19th century due to over-hunting. Two papers, one lead by Chih-Ming Hung published in PNAS, and one by Gemma Murray published in Nature, produced genome data from museum specimens and from related extant pigeon species. Both studies showed surprisingly low genomic diversity indicative of a low effective population size. They differ in what they think caused this low diversity, with Hung et al. (2014) pointing to population fluctuations, and Murray et al. (2017) inferring pervasive natural selection. I haven’t looked at the details to decide which is more likely to be correct, but either way, this is a remarkable example of low diversity in a high abundance species, and a great use of museum sequencing.

Genomes come in all sizes and levels of complexity, and I think there’s something to learn from sequencing them all. From tiny desiccation-tolerant bdelloid rotifers (Nowell et al. 2018) and wonderful water bears (Koutsovoulos et al. 2016), to enigmatic Gnetum (one to look up, plant fans, see Wan et al. 2018) and giant lilly genomes (Kelly et al. 2015), each with their own fascinating biology. The next time whole genome sequencing fatigue sets in as you see the boiler plate title “the genome of XXX reveals YYY”, remember that genome sequencing is a superb tool to make amazing discoveries about the natural world.

References

Fukushima K, Fang X, Alvarez-Ponce D, et al. (2017) Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory. Nature ecology & evolution 1, 0059.

Hung C-M, Shaner P-JL, Zink RM, et al. (2014) Drastic population fluctuations explain the rapid extinction of the passenger pigeon. Proceedings of the National Academy of Sciences 111, 10636-10641.

Kelly LJ, Renny‐Byfield S, Pellicer J, et al. (2015) Analysis of the giant genomes of Fritillaria (Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size. New Phytologist 208, 596-607.

Koutsovoulos G, Kumar S, Laetsch DR, et al. (2016) No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini. Proceedings of the National Academy of Sciences, 201600338.

Murray GG, Soares AE, Novak BJ, et al. (2017) Natural selection shaped the rise and fall of passenger pigeon genomic diversity. Science 358, 951-954.

Nowell RW, Almeida P, Wilson CG, et al. (2018) Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species. PLoS biology 16, e2004830.

Wan T, Liu Z-M, Li L-F, et al. (2018) A genome for gnetophytes and early evolution of seed plants. Nature Plants 4, 82.

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About Alex Twyford

Alex Twyford is a Research Fellow at the University of Edinburgh, and a Research Associate at the Royal Botanic Garden Edinburgh. He studies the ecology and evolution of plants. Twitter @alex_twyford.
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