Imprinting disorders: a group of congenital disorders with overlapping patterns of molecular changes affecting imprinted loci.

Congenital imprinting disorders (IDs) are characterised by molecular changes affecting imprinted chromosomal regions and genes, i.e. genes that are expressed in a parent-of-origin specific manner. Recent years have seen a great expansion in the range of alterations in regulation, dosage or DNA sequence shown to disturb imprinted gene expression, and the correspondingly broad range of resultant clinical syndromes. At the same time, however, it has become clear that this diversity of IDs has common underlying principles, not only in shared molecular mechanisms, but also in interrelated clinical impacts upon growth, development and metabolism. Thus, detailed and systematic analysis of IDs can not only identify unifying principles of molecular epigenetics in health and disease, but also support personalisation of diagnosis and management for individual patients and families.All authors are members of the EUCID.net network, funded by COST (BM1208). TE is funded by the German Ministry of research and education (01GM1513B). GPdN is funded by I3SNS Program of the Spanish Ministry of Health (CP03/0064; SIVI 1395/09), Instituto de Salud Carlos III (PI13/00467) and Basque Department of Health (GV2014/111017).This is the final version of the article. It first appeared from BioMed Central via http://dx.doi.org/10.1186/s13148-015-0143-

Advancing Eucalyptus genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries

<p>Abstract</p> <p>Background</p> <p><it>Eucalyptus </it>species are among the most planted hardwoods in the world because of their rapid growth, adaptability and valuable wood properties. The development and integration of genomic resources into breeding practice will be increasingly important in the decades to come. Bacterial artificial chromosome (BAC) libraries are key genomic tools that enable positional cloning of important traits, synteny evaluation, and the development of genome framework physical maps for genetic linkage and genome sequencing.</p> <p>Results</p> <p>We describe the construction and characterization of two deep-coverage BAC libraries EG_Ba and EG_Bb obtained from nuclear DNA fragments of <it>E. grandis </it>(clone BRASUZ1) digested with <it>Hind</it>III and <it>BstY</it>I, respectively. Genome coverages of 17 and 15 haploid genome equivalents were estimated for EG_Ba and EG_Bb, respectively. Both libraries contained large inserts, with average sizes ranging from 135 Kb (Eg_Bb) to 157 Kb (Eg_Ba), very low extra-nuclear genome contamination providing a probability of finding a single copy gene ≥ 99.99%. Libraries were screened for the presence of several genes of interest <it>via </it>hybridizations to high-density BAC filters followed by PCR validation. Five selected BAC clones were sequenced and assembled using the Roche GS FLX technology providing the whole sequence of the <it>E. grandis </it>chloroplast genome, and complete genomic sequences of important lignin biosynthesis genes.</p> <p>Conclusions</p> <p>The two <it>E. grandis </it>BAC libraries described in this study represent an important milestone for the advancement of <it>Eucalyptus </it>genomics and forest tree research. These BAC resources have a highly redundant genome coverage (> 15×), contain large average inserts and have a very low percentage of clones with organellar DNA or empty vectors. These publicly available BAC libraries are thus suitable for a broad range of applications in genetic and genomic research in <it>Eucalyptus </it>and possibly in related species of <it>Myrtaceae</it>, including genome sequencing, gene isolation, functional and comparative genomics. Because they have been constructed using the same tree (<it>E. grandis </it>BRASUZ1) whose full genome is being sequenced, they should prove instrumental for assembly and gap filling of the upcoming <it>Eucalyptus </it>reference genome sequence.</p

Comprehensive genetic dissection of wood properties in a widely-grown tropical tree: Eucalyptus

Background: Eucalyptus is an important genus in industrial plantations throughout the world and is grown for use as timber, pulp, paper and charcoal. Several breeding programmes have been launched worldwide to concomitantly improve growth performance and wood properties (WPs). In this study, an interspecific cross between Eucalyptus urophylla and E. grandis was used to identify major genomic regions (Quantitative Trait Loci, QTL) controlling the variability of WPs. Results: Linkage maps were generated for both parent species. A total of 117 QTLs were detected for a series of wood and end-use related traits, including chemical, technological, physical, mechanical and anatomical properties. The QTLs were mainly clustered into five linkage groups. In terms of distribution of QTL effects, our result agrees with the typical L-shape reported in most QTL studies, i.e. most WP QTLs had limited effects and only a few (13) had major effects (phenotypic variance explained &gt; 15%). The co-locations of QTLs for different WPs as well as QTLs and candidate genes are discussed in terms of phenotypic correlations between traits, and of the function of the candidate genes. The major wood property QTL harbours a gene encoding a Cinnamoyl CoA reductase (CCR), a structural enzyme of the monolignol-specific biosynthesis pathway. Conclusions: Given the number of traits analysed, this study provides a comprehensive understanding of the genetic architecture of wood properties in this Eucalyptus full-sib pedigree. At the dawn of Eucalyptus genome sequence, it will provide a framework to identify the nature of genes underlying these important quantitative traits. (Résumé d'auteur

Molecular evolution of Adh and LEAFY and the phylogenetic utility of their introns in Pyrus (Rosaceae)

<p>Abstract</p> <p>Background</p> <p>The genus <it>Pyrus </it>belongs to the tribe Pyreae (the former subfamily Maloideae) of the family Rosaceae, and includes one of the most important commercial fruit crops, pear. The phylogeny of <it>Pyrus </it>has not been definitively reconstructed. In our previous efforts, the internal transcribed spacer region (ITS) revealed a poorly resolved phylogeny due to non-concerted evolution of nrDNA arrays. Therefore, introns of low copy nuclear genes (LCNG) are explored here for improved resolution. However, paralogs and lineage sorting are still two challenges for applying LCNGs in phylogenetic studies, and at least two independent nuclear loci should be compared. In this work the second intron of <it>LEAFY </it>and the alcohol dehydrogenase gene (<it>Adh</it>) were selected to investigate their molecular evolution and phylogenetic utility.</p> <p>Results</p> <p>DNA sequence analyses revealed a complex ortholog and paralog structure of <it>Adh </it>genes in <it>Pyrus </it>and <it>Malus</it>, the pears and apples. Comparisons between sequences from RT-PCR and genomic PCR indicate that some <it>Adh </it>homologs are putatively nonfunctional. A partial region of <it>Adh1 </it>was sequenced for 18 <it>Pyrus </it>species and three subparalogs representing <it>Adh1-1 </it>were identified. These led to poorly resolved phylogenies due to low sequence divergence and the inclusion of putative recombinants. For the second intron of <it>LEAFY</it>, multiple inparalogs were discovered for both <it>LFY1int2 </it>and <it>LFY2int2</it>. <it>LFY1int2 </it>is inadequate for phylogenetic analysis due to lineage sorting of two inparalogs. <it>LFY2int2-N</it>, however, showed a relatively high sequence divergence and led to the best-resolved phylogeny. This study documents the coexistence of outparalogs and inparalogs, and lineage sorting of these paralogs and orthologous copies. It reveals putative recombinants that can lead to incorrect phylogenetic inferences, and presents an improved phylogenetic resolution of <it>Pyrus </it>using <it>LFY2int2-N</it>.</p> <p>Conclusions</p> <p>Our study represents the first phylogenetic analyses based on LCNGs in <it>Pyrus</it>. Ancient and recent duplications lead to a complex structure of <it>Adh </it>outparalogs and inparalogs in <it>Pyrus </it>and <it>Malus</it>, resulting in neofunctionalization, nonfunctionalization and possible subfunctionalization. Among all investigated orthologs, <it>LFY2int2-N </it>is the best nuclear marker for phylogenetic reconstruction of <it>Pyrus </it>due to suitable sequence divergence and the absence of lineage sorting.</p

Coalescent Simulations Reveal Hybridization and Incomplete Lineage Sorting in Mediterranean Linaria

We examined the phylogenetic history of Linaria with special emphasis on the Mediterranean sect. Supinae (44 species). We revealed extensive highly supported incongruence among two nuclear (ITS, AGT1) and two plastid regions (rpl32-trnLUAG, trnS-trnG). Coalescent simulations, a hybrid detection test and species tree inference in *BEAST revealed that incomplete lineage sorting and hybridization may both be responsible for the incongruent pattern observed. Additionally, we present a multilabelled *BEAST species tree as an alternative approach that allows the possibility of observing multiple placements in the species tree for the same taxa. That permitted the incorporation of processes such as hybridization within the tree while not violating the assumptions of the *BEAST model. This methodology is presented as a functional tool to disclose the evolutionary history of species complexes that have experienced both hybridization and incomplete lineage sorting. The drastic climatic events that have occurred in the Mediterranean since the late Miocene, including the Quaternary-type climatic oscillations, may have made both processes highly recurrent in the Mediterranean flora

Heterozygous ANKRD17 loss-of-function variants cause a syndrome with intellectual disability, speech delay, and dysmorphism

ANKRD17 is an ankyrin repeat-containing protein thought to play a role in cell cycle progression, whose ortholog in Drosophila functions in the Hippo pathway as a co-factor of Yorkie. Here, we delineate a neurodevelopmental disorder caused by de novo heterozygous ANKRD17 variants. The mutational spectrum of this cohort of 34 individuals from 32 families is highly suggestive of haploinsufficiency as the underlying mechanism of disease, with 21 truncating or essential splice site variants, 9 missense variants, 1 in-frame insertion-deletion, and 1 microdeletion (1.16 Mb). Consequently, our data indicate that loss of ANKRD17 is likely the main cause of phenotypes previously associated with large multi-gene chromosomal aberrations of the 4q13.3 region. Protein modeling suggests that most of the missense variants disrupt the stability of the ankyrin repeats through alteration of core structural residues. The major phenotypic characteristic of our cohort is a variable degree of developmental delay/intellectual disability, particularly affecting speech, while additional features include growth failure, feeding difficulties, non-specific MRI abnormalities, epilepsy and/or abnormal EEG, predisposition to recurrent infections (mostly bacterial), ophthalmological abnormalities, gait/balance disturbance, and joint hypermobility. Moreover, many individuals shared similar dysmorphic facial features. Analysis of single-cell RNA-seq data from the developing human telencephalon indicated ANKRD17 expression at multiple stages of neurogenesis, adding further evidence to the assertion that damaging ANKRD17 variants cause a neurodevelopmental disorder.Neurolog

Genetic diversity assessment of two <em>Medicago sativa</em> genes: CAD and WXP1

International audienceAlfalfa (Medicago sativa L.) is a major perennial forage legume crop with numerous nutritional and environmental benefits. This allogamous and autotetraploid species whose varieties are synthetic populations, has a highly polymorphic genome and a short linkage disequilibrium. Allele mining strategy on targeted candidate genes is an option to select valuable parents for breeding. In this paper, we assessed allelic diversity of CAD and WXP1 genes, involved in lignin biosynthesis and drought tolerance respectively, in a set of 384 individuals. For CAD which had two splice forms, 30 and 31 variants (out of 1077 and 906 base pairs of the coding sequences, respectively) have been observed including 37 and 52% of non-synonymous mutations. More variants were observed in WXP1 sequence, with 157 observed in WXP1 coding sequence (coding sequence of 1116 base pairs), including 60% non-synonymous mutations. Among the non-synonymous mutations, some probably affected protein function. Both genes were under purifying selection, especially CAD with dN/dS rate of 0.05 and 0.12 for both splice forms, against a rate of 0.26 for WXP1. Difference in variant proportion is probably explained by differential selective pressure that may be induced by contrasted expression levels. Indeed, CAD is highly and continually expressed whereas WXP1 is induced in some specific conditions. Further studies assessing the impact of variants on phenotype will help to conclude on the allele mining strategy in alfalfa breeding