What I’m reading (23-08-2018)

A summary of the plant evolution papers that I’ve enjoyed reading over the last month

Fern genomes elucidate land plant evolution and cyanobacterial symbioses

Ferns are the only major lineage of green plants that do not have a representative genome sequence. As a sister group to seed plants, it is important that this phylogenetic gap is closed for the evolutionary genomic study of plants. Here, Li et al publish the first genomes of two ferns, Azolla filiculoides and Salvinia cucullata. Ferns and gymnosperms are known to have gigantic genomes which has been a roadblock to produce sequence data for these lineages. Azolla and Salvinia have relatively small genomes at 0.75 Gb and 0.26 Gb respectively making them technically and financially feasible. Comparative analysis supports multiple whole genome duplications in ferns, which are likely to be the cause of their large size. Despite this, 20201 and 19914 predicted protein coding genes were identified for Azolla filiculoides and Salvinia cucullata respectively. A large proportion of the both genomes consisted of introns and repetitive sequences. Azolla has a symbiosis with a nitrogen fixing bacteria, Nostoc. Sequencing of bacterial partners revealed clear co-speciation patterns and further analysis found that the cyanobiont confers a resilience to fluctuating nitrogen availability. The implementation of this novel fern data into an existing comparative genomic framework will enhance our understanding of the plant tree of life, leading to powerful insights into gene family diversification.

Nature plants: https://www.nature.com/articles/s41477-018-0188-8.

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Wheat (Triticum aestivum L.) is the most cultivated crop in the world. Therefore maintaining crop yield and sustainability under an ever variable climate is a major priority for food security and the global economy. Genome sequencing of any crop species helps to understand the molecular basis behind important productivity traits. Wheat has a hexaploid genome (with 6 sets of chromosomes) which is 5 times larger than the human genome. This complexity, technological constraints and expense have all been hindrances to producing the bread wheat genome. In this paper, the International Wheat Genome Sequencing Consortium report the genome of Triticum aestivum L. producing an annotated reference sequence assembly containing 94% coverage with 107,891 predicted high-confidence genes. Loci were identified that control resistance to abiotic stress, flowering time and susceptibility to insect damage which are potential avenues for future research. The production of this high quality genome is an excellent resource to improve our understanding of wheat biology and breeding. Sequence-level data can now be accessed to untangle the expression of complex plant traits. A deeper understanding about the impacts of whole genome duplications on plant biology can also be gained.

Science: http://science.sciencemag.org/content/361/6403/eaar7191.

Bread wheat

Other papers I’ve enjoyed recently

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