Balanced Gene Losses, Duplications and Intensive Rearrangements Led to an Unusual Regularly Sized Genome in Arbutus unedo Chloroplasts

Abstract

Completely sequenced plastomes provide a valuable source of information about the duplication, loss, and transfer events of chloroplast genes and phylogenetic data for resolving relationships among major groups of plants. Moreover, they can also be useful for exploiting chloroplast genetic engineering technology. Ericales account for approximately six per cent of eudicot diversity with 11,545 species from which only three complete plastome sequences are currently available. With the aim of increasing the number of ericalean complete plastome sequences, and to open new perspectives in understanding Mediterranean plant adaptations, a genomic study on the basis of the complete chloroplast genome sequencing of Arbutus unedo and an updated phylogenomic analysis of Asteridae was implemented. The chloroplast genome of A. unedo shows extensive rearrangements but a medium size (150,897 nt) in comparison to most of angiosperms. A number of remarkable distinct features characterize the plastome of A. unedo: five-fold dismissing of the SSC region in relation to most angiosperms; complete loss or pseudogenization of a number of essential genes; duplication of the ndhH-D operon and its location within the two IRs; presence of large tandem repeats located near highly re-arranged regions and pseudogenes. All these features outline the primary evolutionary split between Ericaceae and other ericalean families. The newly sequenced plastome of A. unedo with the available asterid sequences allowed the resolution of some uncertainties in previous phylogenies of Asteridae.

The complete chloroplast genome sequence ofHelwingia himalaica(Helwingiaceae, Aquifoliales) and a chloroplast phylogenomic analysis of the Campanulidae

“…Comparing with other angiosperm chloroplast genomes, more repeats and tRNA genes occurred near rearrangement endpoints in this species. The positive connection between rearrangement and repeated sequences has also been found in other plants, like Arbutus unedo (Martínez-Alberola et al, 2013), Geraniaceae (Weng et al, 2013), Vaccinium macrocarpon (Fajardo et al, 2013) and cupressophytes (Wu & Chaw, 2014). However, the effects of these chloroplast gene rearrangements on plant physical functions still need more study.…”

On the brink: the highly reduced plastomes of nonphotosynthetic Ericaceae

“…Furthermore, the accD gene has been reduced to very short pseudogenes ( c . 200–300 bp) in photosynthetic Ericaceae (Fajardo et al ., ; Martinez‐Alberola et al ., ), which indicates a single (functional) loss of this gene within the family. Recently, Logacheva et al .…”

“…Another gene commonly found in the plastomes of heterotrophs is clpP , which encodes a protease subunit involved in ATP‐dependent degradation of photosynthetic complexes (Peltier et al ., ; Lam et al ., ). clpP is found as a pseudogene in Arbutus unedo , the closest autotrophic relative to MH Ericaceae (Martinez‐Alberola et al ., ; Freudenstein et al ., ; Lallemand et al ., ), which suggests that a clpP pseudogene is a pleisomorphic state. However, clpP exists as a highly divergent ORF in most MH Ericaceae.…”

Passifloraplastome sequencing reveals widespread genomic rearrangements

“…Smaller fluctuations in IR boundaries of 1–2 kb due to IR expansion and contraction are very common in seed plants (Downie & Jansen, ). Larger variation in plastome size due to IR expansion and contraction has been documented in several unrelated lineages, including Geraniaceae (Chumley et al, ; Blazier et al, ; Weng et al, , 2017), Plantago (Zhu et al, ), Ericaceae (Fajardo et al, ; Martínez‐Alberola et al, ), Berberis (Ma et al, ), Annona (Blazier et al, ) and Trochodendraceae (Sun et al, ). Among these lineages, Geraniaceae has the broadest range of IR sizes including species with enormous IR expansion to ∼88 kb in Pelargonium transvaalense (Weng et al, ), significant reduction to ∼7 kb in Monsonia speciosa (Guisinger et al, ) and species lacking an IR entirely in Erodium and Monsonia (Blazier et al, ; Ruhlman et al, ).…”