The avocado genome informs deep angiosperm phylogeny

Avocados, the green gold in worldwide agriculture. The avocado genome has been sequenced by an international team in which the researchers Julio Rozas and Alejandro Sáncez-Gracia, from the Faculty of Biology and the Biodiversity Research Institute of the

The avocado genome informs deep angiosperm phylogeny

The avocado genome has been sequenced by an international team in which the researchers Julio Rozas and Alejandro Sáncez-Gracia, from the Faculty of Biology and the Biodiversity Research Institute of the UB (IRBio), and members of the platform Bioinformatics Barcelona (BIB) have taken part too.

The new study, published in the journal Proceedings of the National Academy of Science (PNAS), will help improve the programs of genetic modification to optimize the growth of this plant -green gold in the international market- and promote its resistance towards pathogenic agents and diseases, among other aspects.

The study counts on other participants from about twenty institutions, under the supervision of the researchers Luis Herrera-Estrella (Center for Research and Advanced Studies of the National Polytechnic Institute, Mexico), and Víctor A. Albert, from the University of Buffalo (New York, United States).

Avocados, the green gold in worldwide agriculture

People have eaten this tropical fruit from the Persea genera -grown in South America, since pre-Columbian times- a lot over the years, and its consumption has increased worldwide and has generated an economic interest in the international market. The international team has sequenced the genome of two avocado plants, the Mexican variety (Persea americana var. drymifolia) and the most popular culture one (Persea americana Mill. cv. Hass).

The genome of this tropical plant -organized in 12 chromosomes known so far-, has a size of 920 Mb, with little variations among the studied models, according to the new study. "The most relevant element of the genomic structure of the avocado is its history of complete genome duplications", notes Julio Rozas, professor of Genetics and together with Alejandro Sánchez-Gracia, co-director of the Research Group on Evolutionary Genomics and Bioinformatics at the Department of Genetics, Microbiology and Statistics of the UB and IRBio.

In particular, the experts compared the syntenic relationship -the order in which the genes are conserved and positioned in the chromosomes- between the avocado genomes and the species Amborella trichopoda Baill 1869. This species -an endemic plant from New Caledonia- is considered to be the only current representative of the most primitive lineage of flowering plants and angiosperms. In this primitive angiosperm, there are no signs of complete genome duplications, therefore it is the source of the study of genomic duplication evolution for all other flowering plants. 

Tandem duplications and resistance to attacks from pathogens

According to the results, "for one region of the analysed genome, there are four copies of the genomic fragments in the avocado, and one copy in Amborella. This suggests the avocado genome has undergone two complete genome duplication processes", says the researcher Alejandro Sánchez-Gracia (UB-IRBio).    

These recent tandem duplications are involved in adaption metabolic responses of the avocado towards the attack of fungal pathogens, according to the authors. "At the same time, those duplications that appeared during the complete genome duplications -and which are maintained due natural selection- seem to be involved in basic aspects of the plant's development and physiology", notes Sánchez-Gracia.  

Discovering the phylogenetic tree of angiosperm plants

There are still many doubts on the origins and evolution of the avocado plant, a species that belongs to the magnolia genus. The new study profiles a new scenario to find its phylogenetic position in the evolutionary tree of angiosperms, in particular regarding some eudicot species with great economic interest within agriculture, such as coffee (Coffea), or tomato (Solanum), or grapevine (Vitis), which share more genetic compounds among them than with the avocado.  

In this group of plants, the diversification process was fast and it made the phylogenetic analysis difficult. Through a comprehensive phylogenomic analysis of nineteen angiosperm species -with different molecular markers- the new study reveals that the avocado plant is a sibling of the monocotyledon and eudicots families (coffee, tomato, grapevines). 

"The only genetic compounds all these species share are those defining all angiosperms and differentiating from gymnosperms and non-seed plants", notes researcher Pablo Librado, former PhD student of the University of Barcelona and co-author of the study, now member of the Center for Geogenetics of the University of Copenhagen and the Natural History Museum of Denmark. 

From genomic libraries to the Biocomputing software created in the UB

For the sequencing of the Mexican variation, researchers used different genomic libraries and sequencing technology, such as the Bacterial Artificial Cromosome (BAC) or the Illumina platform HiSeq, which provide a great coverage of the studied genome. In Hass, they used the PacBio sequencing methodology (single-molecule real-time-SMRT) with high quality DNA.

The population analysis based on the study of single nucleotide polymorphisms (SNP) enabled getting an insight of the genetic composition and history of the commercial variety Hass, the result of the introgression of genetic material from Guatemala -selective sweeps- in the genomic background of the Mexican avocado.

In the study, the UB-IRBio experts carried out a phylogenomic analysis consisting on the determination of single-copy orthologues and trees with information on aminoacid sequencings and coding nucleotides for this group of genes. A great part of this study was focused on the analysis of the dynamics on the gene loss and origin through BadiRate, a Biocomputing software carried out at the UB by the experts Julio Rozas and Pablo Librado.  

Improving agricultural productivity in world crops

The new study brings a new essential perspective to conduct association studies on the species genome and to find the genes -and different genetic variants- that determine the most relevant features for the economy and productivity of agriculture.  

In this context, the Research Group on Evolutionary Genomics and Bioinformatics of the UB conducted several scientific collaborations with the team of the lecturer Víctor A. Albert, among which stands out the study that identified genetic changes that enabled the adaption of carnivorous diet in different plants (Nature Ecology & Evolution, 2017), an evolutionary process that has been independently repeated in several species using the same molecular solutions.

The UB-IRBio team of experts had a distinguished participation in the sequencing of the genomes of different organisms such as the tick (Ixodes scapularis), centipede (Strigamia maritima), coffee (Coffea canephora), and the body louse (Pediculus humanus humanus), among others.
 

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