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    Black cottonwood trees can clone themselves to produce offspring that are connected to their parents by the same root system. Now, it turns out that the connected clones have many genetic differences, even tissues from the top and bottom of a single tree carry mutations.

    “The variation within a tree is as great as the variation across unrelated trees,” says Ken Paige, who led the study that made the discovery.

    “This could change the classic paradigm that evolution only happens in a population rather than at an individual level,” says Brett Olds from the University of Illinois at Urbana-Champaign, who presented the team's research at the 2012 Ecological Society of America Annual Meeting in Portland, Oregon.

    These somatic mutations – that occur in cells other than sperm or eggs – are familiar to horticulturalists, who have long bred new plant varieties by grafting mutant branches onto ‘normal’ stocks. But until now, no one has catalogued the total number of somatic mutations in an individual plant. “Most of the research hasn’t been genome-wide. It’s usually a certain region or certain genes,” says Olds. “This is the first one across entire genomes.”

    The black cottonwood is the ideal species for such a study. It lives for up to 200 years and grows to 30-50 metres, so its tissues are separated by long distances and long spans of growth - and it forms connected clones. In 2006, it became the first tree to have its full genome sequenced [1].

    Olds collected samples from eleven black cottonwood parents and their connected offspring. For each one, he sequenced the full genomes of tissues from the highest buds, lowest branches, and roots. “Five years ago, this kind of project would have been prohibitively expensive,” says Ari Novy, a plant biologist from the US Botanic Gardens in Washington DC, who was not involved in the study. “Olds has made great use of next-generation sequencing technology.”

    When Olds compared these sequences to the reference cottonwood genome, he found 188,000 mutations that were unique to just one tissue sample, differing even from other parts of the same tree. Of these, 8,600 mutations fell within a gene, and 5,500 changed an amino acid in the resulting proteins.

    “We may have to expand our conception of an organism’s genome to allow for extensive somatic mutation among cell lines within that organism, as part of the process of development,” Novy says. “When people study plants, they‘ll often take a cutting from a leaf and assume that it is representative of the plant’s genome,” says Olds. “That may not be the case. You may need to take multiple tissues.”

    Other surprises emerged when Olds used the tissue-specific amino acid changes to build a family tree of the different cottonwood tissues. In one tree, the top buds of the parent and offspring were genetically closer to each other than to their respective roots or lower branches. In another tree, the top bud was closer to the reference cottonwood genome than to any of the other tissues from the same individual.

    Olds thinks that many of the mutations would be harmful, causing the tree to destroy its own mutated tissues, or alter the way it controls its genes. This could explain why many of the tissue-specific mutations affected genes involved in cell death, immune responses, metabolism and DNA binding.

    The findings reveal intriguing parallels to cancer. Earlier this year, British scientists showed that separate parts of the same tumour can evolve independently and build up distinct genetic mutations, meaning that single biopsies only give a narrow view of the tumour’s diversity (see “Biopsy gives only a snapshot of tumour diversity ”) [2].

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    cottonwood. Nature (2012). https://doi.org/10.1038/nature.2012.11156

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