Genomics of the origin and evolution of CitrusGuohong albert Wu 1 , Javier Terol 2 , Victoria ibanez 2 , antonio López-García 2 , estela Pérez-román 2 , carles borredá 2 , concha Domingo 2 , francisco r. Tadeo 2 , Jose carbonell-caballero 3 , roberto alonso 3 , franck curk 4 , Dongliang Du 5 , Patrick Ollitrault 6 , Mikeal L. roose 7 , Joaquin Dopazo 3,8 , frederick G. Gmitter Jr 5 , Daniel S. rokhsar 1,9,10 & Manuel Talon 2The genus Citrus and related genera (Fortunella, Poncirus, Eremocitrus and Microcitrus) belong to the angiosperm subfamily Aurantioideae of the Rutaceae family, which is widely distributed across the monsoon region from west Pakistan to north-central China and south through the East Indian Archipelago to New Guinea and the Bismarck Archipelago, northeastern Australia, New Caledonia, Melanesia and the western Polynesian islands 1 . Native habitats of citrus and related genera roughly extend throughout this broad area (Extended Data Fig. 1a and Supplementary Table 1), although the geogra phical origin, timing and dispersal of citrus species across southeast Asia remain unclear. A major obstacle to resolving these uncertainties is our poor understanding of the genealogy of complex admixture in cultivated citrus, as has recently been shown 2 . Some citrus are clonally propagated apomictically 3 through nucellar embryony, that is, the development of non-sexual embryos originating in the maternal nucellar tissue of the ovule, and this natural process may have been co-opted during domestication; grafting is a relatively recent phenomenon 4 . Both modes of clonal propagation have led to the domestication of fixed (desirable) genotypes, including interspecific hybrids, such as oranges, limes, lemons, grapefruits and other types.Under this scenario, it is not surprising that the current chaotic citrus taxonomy-based on long-standing, conflicting proposals 5,6 -requires a solid reformulation consistent with a full understanding of the hybrid and/or admixture nature of cultivated citrus species. Here we analyse genome sequences of diverse citrus to characterize the diversity and evolution of citrus at the species level and identify citrus admixtures and interspecific hybrids. We further examine the network of relatedness among mandarins and sweet orange, as well as the pattern of the introgression of pummelos among mandarins for clues to the early stages of citrus domestication. Diversity and evolution of the genus CitrusTo investigate the genetic diversity and evolutionary history of citrus, we analysed the genomes of 58 citrus accessions and two outgroup genera (Poncirus and Severinia) that were sequenced to high coverage, including recently published sequences 2,3,7 as well as 30 new genome sequences described here. For our purpose, we do not include accessions related by somatic mutations. These sequences represent a diverse sampling of citrus species, their admixtures and hybrids (Supplementary Tables 2, 3 and Supplementary Notes 1, 2). Our collection includes accessions from eight previously unsequ...
Our results demonstrate the existence of an endometrial microbiota that is highly stable during the acquisition of endometrial receptivity. However, pathological modification of its profile is associated with poor reproductive outcomes for in vitro fertilization patients. This finding adds a novel microbiological dimension to the reproductive process.
Citrus 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 (insertions and deletions), 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 analyzed 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.
(Abstracted from Am J Obstet Gynecol 2016;215(6):684–703) In 2002, the vaginal microbiota was first identified using molecular methods that allowed detection of nonculturable bacteria. Alterations in vaginal microbiota could have clinical implications for reproductive and obstetric processes.
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