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Monday, April 6, 2020
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Genomes galore!

We’re not usually that big on plant genomes (“the complete set of genetic information in an organism”) in Cuttings items. We know what they are, and appreciate their importance, but until those genomes are translated into known functions for all the genes identified, etc. there’s not as much of a story as we’d like. However, sometimes one simply can’t ignore them. And, lately there’s been such a veritable tsunami of phytogenomic ‘firsts’, it would be remiss of us if we didn’t make some acknowledgement of their existence. However, since there are so many of them to report, we don’t have the space to offer the usual insightful Cuttingsesque commentary. But, here goes…

DNA concept
Here come the genomes. Image: Canva.

Pteridophytes are represented by the sequencing of genomes of two fern species – Azolla filiculoides and Salvinia cucullata – by Fay-Wei Li et al.. And one of the most fascinating features of this achievement is that the initial costs of sequencing were sought via ‘crowd-funding’, which event was covered by P Cuttings back in 2014. The significance and relevance of this sequencing breakthrough has been interpreted for us by Jo Ann Banks.

Ascending the plant evolutionary ladder, to gymnosperms, Tao Wan et al. report “a high-quality draft genome sequence for Gnetum montanum, the first for any gnetophyte”. Expert interpretation of which coup is provided by Michael Barker.

Next we share a selection of angiosperm genomes. First, although in no particular order, we have not one but two genomes for the same species of rose, Rosa chinensis – and not just the same species, but the same cultivar “Old Blush” – by Olivier Raymond et al. and L. Hibrand Saint-Oyant et al..

Guiding us – hopefully – through the mysteries of why we have, or need, two genome sequences* of the same organism, we have commentary by Aureliano Bombarely. Although no excuse is surely needed to study genomes of plants, it seems incumbent upon the authors of such work to provide that ‘justification’ (or maybe this rationale is necessary to ensure publication in ‘high impact journals’). Accordingly, we have the genome of Cuscuta australis – a type of dodder, a parasitic angiosperm – from Guiling Sun et al., that “sheds light on evolution of plant parasitism”.

In similar vein, insights into the famous longevity of trees is anticipated with publication of the genome of an oak (Quercus robur) by Christophe Plomion et al..

Arguably, one of the most important plants from a feeding-the-world point of view is rice: “Billions of people around the world rely on rice as a mainstay of their diet. The grain provides about 20 percent of the calories consumed by humans worldwide”. Contributing important knowledge and insights for efforts to improve such factors as the nutritional quality of this cereal is the release of genomes of 13 rice species (yes, there’s more to this grain than just Oryza sativa) by Joshua Stein et al..

Another monocot that, like rice, famously also provides calories to humans – albeit from its sugar content whose consequences are more health-threatening, rather than health-promoting and life-sustaining than for rice – is sugarcane, whose genomes was announced by Olivier Garsmeur et al..

What links all of the above genomes is that they are from members of the Plantae, the Plant Kingdom**, i.e. the primarily terrestrial-inhabiting, so-called land plants (or Embryophyta). We’ve not always had such plants on the planet; indeed, the general notion is that a land flora evolved about 500 MYA. But, if evolution is correct, something will have given rise to those first land-dwelling plants, but what?

In keeping with the idea that an ancient, aquatic green algal-like organism has that honour, Tomoaki Nishotama et al. have sequenced the genome of Chara braunii. In their own unique way each of the genomes mentioned contributes to the ambitions of the 10KP (10,000 Plants) Genome Sequencing Project, which aims to sequence and characterize representative genomes from every major clade of embryophytes, green algae, and protists (excluding fungi) within the next 5 years. Anyway, that’s it – for now, but, one suspects, not for long! – for the ‘PC’ [Plant Cuttings…] guide to all that’s happening in the rapidly evolving world of plant genomics.

* The phenomenon whereby two genomes for the same organism are published at more or less the same time is not that rare in plant science – as we covered in 2013 for chickpea (Cicer arietinum), and for pigeon pea (Cajanus cajan) in 2012.

** That, and the fact that they also all happen to have been published in the Nature family of journals…

Nigel Chaffeyhttps://www.bathspa.ac.uk/our-people/nigel-chaffey/
Nigel is a botanist and was a full-time academic at Bath Spa University (Bath, near Bristol, UK) until 31st July, 2019. As News Editor for the Annals of Botany he contributed the monthly Plant Cuttings column to that august international botanical organ (until March 2019). He remains a botanist and is now a freelance plant science communicator who continues to share his Cuttingsesque items with a plant-curious audience. In that guise his main goal is to inform (hopefully, in an educational, and entertaining way...) about plants and plant-people interactions.

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