02581nas a2200517   4500008004100000022001400041245005200055210005100107260001500158300001200173490000800185520112500193653002301318653001701341653001101358653002001369653002501389653002301414653001801437653001301455653001501468653001701483653002101500653002001521653002701541653001401568100002401582700001801606700002201624700002801646700002601674700002101700700002001721700002401741700003101765700002001796700001701816700001801833700002401851700002101875700002001896700002601916700002301942700001801965856008001983       2018                        eng d  a1476-468700aGenomics of the origin and evolution of Citrus.0 aGenomics of the origin and evolution of Citrus  c2018 02 15  a311-3160 v5543 a<p>The genus Citrus, comprising some of the most widely cultivated fruit crops worldwide, includes an uncertain number of species. Here we describe ten natural citrus species, using genomic, phylogenetic and biogeographic analyses of 60 accessions representing diverse citrus germ plasms, and propose that citrus diversified during the late Miocene epoch through a rapid southeast Asian radiation that correlates with a marked weakening of the monsoons. A second radiation enabled by migration across the Wallace line gave rise to the Australian limes in the early Pliocene epoch. Further identification and analyses of hybrids and admixed genomes provides insights into the genealogy of major commercial cultivars of citrus. Among mandarins and sweet orange, we find an extensive network of relatedness that illuminates the domestication of these groups. Widespread pummelo admixture among these mandarins and its correlation with fruit size and acidity suggests a plausible role of pummelo introgression in the selection of palatable mandarins. This work provides a new evolutionary framework for the genus Citrus.</p>10aAsia, Southeastern10aBiodiversity10acitrus10aCrop Production10aEvolution, Molecular10aGenetic Speciation10aGenome, Plant10aGenomics10aHaplotypes10aHeterozygote10aHistory, Ancient10aHuman Migration10aHybridization, Genetic10aPhylogeny1 aWu, Guohong, Albert1 aTerol, Javier1 aIbañez, Victoria1 aLópez-García, Antonio1 aPérez-Román, Estela1 aBorredá, Carles1 aDomingo, Concha1 aTadeo, Francisco, R1 aCarbonell-Caballero, José1 aAlonso, Roberto1 aCurk, Franck1 aDu, Dongliang1 aOllitrault, Patrick1 aRoose, Mikeal, L1 aDopazo, Joaquin1 aGmitter, Frederick, G1 aRokhsar, Daniel, S1 aTalon, Manuel  uhttps://www.clinbioinfosspa.es/content/genomics-origin-and-evolution-citrus01104nas a2200241   4500008004100000022001400041245015500055210006900210260000800279300000700287490000700294520032500301100001800626700002200644700002100666700002000687700002700707700002700734700001700761700002000778700001800798856004600816       2015                        eng d  a1471-216400aInvolvement of a citrus meiotic recombination TTC-repeat motif in the formation of gross deletions generated by ionizing radiation and MULE activation0 aInvolvement of a citrus meiotic recombination TTCrepeat motif in  cFeb  a690 v163 aTransposable-element mediated chromosomal rearrangements require the involvement of two transposons and two double-strand breaks (DSB) located in close proximity. In radiobiology, DSB proximity is also a major factor contributing to rearrangements. However, the whole issue of DSB proximity remains virtually unexplored.1 aTerol, Javier1 aIbañez, Victoria1 aCarbonell, José1 aAlonso, Roberto1 aEstornell, Leandro, H.1 aLicciardello, Concetta1 aGut, Ivo, G.1 aDopazo, Joaquin1 aTalon, Manuel  uhttps://doi.org/10.1186/s12864-015-1280-302538nas a2200241   4500008004100000022001400041245015600055210006900211260001600280300000700296490000700303520174800310100001802058700002202076700002102098700002002119700002602139700002702165700001602192700002102208700001802229856004902247       2015                        eng d  a1471-216400aInvolvement of a citrus meiotic recombination TTC-repeat motif in the formation of gross deletions generated by ionizing radiation and MULE activation.0 aInvolvement of a citrus meiotic recombination TTCrepeat motif in  c2015 Feb 13  a690 v163 aBACKGROUND: Transposable-element mediated chromosomal rearrangements require the involvement of two transposons and two double-strand breaks (DSB) located in close proximity. In radiobiology, DSB proximity is also a major factor contributing to rearrangements. However, the whole issue of DSB proximity remains virtually unexplored. RESULTS: Based on DNA sequencing analysis we show that the genomes of 2 derived mutations, Arrufatina (sport) and Nero (irradiation), share a similar 2 Mb deletion of chromosome 3. A 7 kb Mutator-like element found in Clemenules was present in Arrufatina in inverted orientation flanking the 5’ end of the deletion. The Arrufatina Mule displayed "dissimilar" 9-bp target site duplications separated by 2 Mb. Fine-scale single nucleotide variant analyses of the deleted fragments identified a TTC-repeat sequence motif located in the center of the deletion responsible of a meiotic crossover detected in the citrus reference genome. CONCLUSIONS: Taken together, this information is compatible with the proposal that in both mutants, the TTC-repeat motif formed a triplex DNA structure generating a loop that brought in close proximity the originally distinct reactive ends. In Arrufatina, the loop brought the Mule ends nearby the 2 distinct insertion target sites and the inverted insertion of the transposable element between these target sites provoked the release of the in-between fragment. This proposal requires the involvement of a unique transposon and sheds light on the unresolved question of how two distinct sites become located in close proximity. These observations confer a crucial role to the TTC-repeats in fundamental plant processes as meiotic recombination and chromosomal rearrangements.1 aTerol, Javier1 aIbañez, Victoria1 aCarbonell, José1 aAlonso, Roberto1 aEstornell, Leandro, H1 aLicciardello, Concetta1 aGut, Ivo, G1 aDopazo, Joaquín1 aTalon, Manuel  uhttp://www.biomedcentral.com/1471-2164/16/6902086nas a2200253   4500008004100000022001400041245014200055210006900197260001600266300001400282490000700296520127300303653001601576653001101592653001401603653000801617100003101625700002001656700002201676700001801698700001801716700002001734856007801754       2015                        eng d  a1537-171900aA phylogenetic analysis of 34 chloroplast genomes elucidates the relationships between wild and domestic species within the genus Citrus.0 aphylogenetic analysis of 34 chloroplast genomes elucidates the r  c2015 Apr 14  a2015-20350 v323 aCitrus genus includes some of the most important cultivated fruit trees worldwide. Despite being extensively studied because of its commercial relevance, the origin of cultivated citrus species and the history of its domestication still remain an open question. Here we present a phylogenetic analysis of the chloroplast genomes of 34 citrus genotypes which constitutes the most comprehensive and detailed study to date on the evolution and variability of the genus Citrus. A statistical model was used to estimate divergence times between the major citrus groups. Additionally, a complete map of the variability across the genome of different citrus species was produced, including single nucleotide variants, heteroplasmic positions, indels and large structural variants. The distribution of all these variants provided further independent support to the phylogeny obtained. An unexpected finding was the high level of heteroplasmy found in several of the analysed genomes. The use of the complete chloroplast DNA not only paves the way for a better understanding of the phylogenetic relationships within the Citrus genus, but also provides original insights into other elusive evolutionary processes such as chloroplast inheritance, heteroplasmy and gene selection.10achloroplast10acitrus10aPhylogeny10aWGS1 aCarbonell-Caballero, José1 aAlonso, Roberto1 aIbañez, Victoria1 aTerol, Javier1 aTalon, Manuel1 aDopazo, Joaquin  uhttp://mbe.oxfordjournals.org/content/early/2015/04/27/molbev.msv082.full