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Spanish Team Presents Citrus Phylogeny Based on Complete Chloroplast Genomes

lemon tree, Madrid

NEW YORK (GenomeWeb) – In a study published in Molecular Biology and Evolution last night, Spanish researchers presented findings from a phylogenetic study of nearly three-dozen citrus plants.

Using chloroplast genome sequences for plants from 30 Citrus species — along with new whole-genome sequences for two mandarin and two pummelo plants — the team looked at relationships between citrus plants as well as genetic variability and signals of selection within the lineage.

Results from the analysis pointed to the presence of three main citrus clades, which diverged from ancestral plants between roughly 6.3 million and 7.5 million years and continued to diverge and radiate during at least two subsequent stretches of evolution.

"The use of complete chloroplast DNA not only paves the way for a better understanding of the phylogenetic relationships within the Citrus genus, but also provides insights into other elusive evolutionary processes such as chloroplast inheritance, heteroplasmy, and gene selection," senior author Joaquin Dopazo, a computational genomics researcher with Spain's Centro de Investigación Príncipe Felipe, and his co-authors wrote.

The team did paired-end Illumina sequencing on chloroplast genomes from lemon, orange, grapefruit, lime, mandarin, kumquat, and two-dozen other Citrus plants. It also considered genome sequences for Mangshan and Huanglingmiao mandarin plants and Guanxi and Shatian pummelo plants that were reported with the 2013 publication of the sweet orange draft genome paper in Nature Genetics.

Based on more than 1,500 high-quality SNPs detected in the chloroplast genomes, the researchers put together a phylogeny for all 34 citrus genotypes.

Their findings suggest citrus ancestors arose some 6.3 million to 7.5 million years ago, followed by divergence into three clades: one comprised of citron and Australian species, another containing micrantha and pummelo representatives, and a third made up of mandarin and papeda plants.

During a more recent radiation that took place an estimated 3.7 million to 5 million years ago, they determined that citrons and Australian citrus plants split from one another, as did mandarin plants and a group of plants containing Pummelos and Papedas species.

Radiation within the citrus groups continued during a third period of evolution that took place some 200,000 to 1.5 million years ago, the team concluded, leading to new species within the mandarin group, for example.

The researchers also described at least half a dozen chloroplast genes that are particularly prone to sequence and/or structural variation, including four genes showing signs of positive selection in one or more citrus groups.

The latter set included the matk and ndhF — genes showing signs of positive selection in Australian citrus species that have become acclimated to dry growing conditions — and the ccsA and ycf1 genes, which appeared to be under positive selection in the mandarin clade and the papeda/mandarin clade, respectively.

The study's authors noted that their chloroplast-based analysis looks at the maternal side of citrus evolution, likely grouping hybrid plants with their maternal species. Still, they argued that the work is "the most comprehensive and detailed study to date on the evolution and variability of the genus Citrus."