Arus P

References (5)

Title : Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence - Alioto_2020_Plant.J_101_455
Author(s) : Alioto T , Alexiou KG , Bardil A , Barteri F , Castanera R , Cruz F , Dhingra A , Duval H , Fernandez IMA , Frias L , Galan B , Garcia JL , Howad W , Gomez-Garrido J , Gut M , Julca I , Morata J , Puigdomenech P , Ribeca P , Rubio Cabetas MJ , Vlasova A , Wirthensohn M , Garcia-Mas J , Gabaldon T , Casacuberta JM , Arus P
Ref : Plant J , 101 :455 , 2020
Abstract : We sequenced the genome of the highly heterozygous almond Prunus dulcis cv. Texas combining short- and long-read sequencing. We obtained a genome assembly totaling 227.6 Mb of the estimated almond genome size of 238 Mb, of which 91% is anchored to eight pseudomolecules corresponding to its haploid chromosome complement, and annotated 27 969 protein-coding genes and 6747 non-coding transcripts. By phylogenomic comparison with the genomes of 16 additional close and distant species we estimated that almond and peach (Prunus persica) diverged around 5.88 million years ago. These two genomes are highly syntenic and show a high degree of sequence conservation (20 nucleotide substitutions per kb). However, they also exhibit a high number of presence/absence variants, many attributable to the movement of transposable elements (TEs). Transposable elements have generated an important number of presence/absence variants between almond and peach, and we show that the recent history of TE movement seems markedly different between them. Transposable elements may also be at the origin of important phenotypic differences between both species, and in particular for the sweet kernel phenotype, a key agronomic and domestication character for almond. Here we show that in sweet almond cultivars, highly methylated TE insertions surround a gene involved in the biosynthesis of amygdalin, whose reduced expression has been correlated with the sweet almond phenotype. Altogether, our results suggest a key role of TEs in the recent history and diversification of almond and its close relative peach.
ESTHER : Alioto_2020_Plant.J_101_455
PubMedSearch : Alioto_2020_Plant.J_101_455
PubMedID: 31529539
Gene_locus related to this paper: prupe-m5wr61

Title : The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution - Verde_2013_Nat.Genet_45_487
Author(s) : Verde I , Abbott AG , Scalabrin S , Jung S , Shu S , Marroni F , Zhebentyayeva T , Dettori MT , Grimwood J , Cattonaro F , Zuccolo A , Rossini L , Jenkins J , Vendramin E , Meisel LA , Decroocq V , Sosinski B , Prochnik S , Mitros T , Policriti A , Cipriani G , Dondini L , Ficklin S , Goodstein DM , Xuan P , Del Fabbro C , Aramini V , Copetti D , Gonzalez S , Horner DS , Falchi R , Lucas S , Mica E , Maldonado J , Lazzari B , Bielenberg D , Pirona R , Miculan M , Barakat A , Testolin R , Stella A , Tartarini S , Tonutti P , Arus P , Orellana A , Wells C , Main D , Vizzotto G , Silva H , Salamini F , Schmutz J , Morgante M , Rokhsar DS
Ref : Nat Genet , 45 :487 , 2013
Abstract : Rosaceae is the most important fruit-producing clade, and its key commercially relevant genera (Fragaria, Rosa, Rubus and Prunus) show broadly diverse growth habits, fruit types and compact diploid genomes. Peach, a diploid Prunus species, is one of the best genetically characterized deciduous trees. Here we describe the high-quality genome sequence of peach obtained from a completely homozygous genotype. We obtained a complete chromosome-scale assembly using Sanger whole-genome shotgun methods. We predicted 27,852 protein-coding genes, as well as noncoding RNAs. We investigated the path of peach domestication through whole-genome resequencing of 14 Prunus accessions. The analyses suggest major genetic bottlenecks that have substantially shaped peach genome diversity. Furthermore, comparative analyses showed that peach has not undergone recent whole-genome duplication, and even though the ancestral triplicated blocks in peach are fragmentary compared to those in grape, all seven paleosets of paralogs from the putative paleoancestor are detectable.
ESTHER : Verde_2013_Nat.Genet_45_487
PubMedSearch : Verde_2013_Nat.Genet_45_487
PubMedID: 23525075
Gene_locus related to this paper: prupe-a0a251pfr7 , prupe-a0a251r634 , prupe-m5x0p5 , prupe-m5xkg4 , prupe-m5x0q4 , prupe-m5vqa7 , prupe-m5wiw5 , prupe-a0a0u2wu32 , prupe-a0a251mtk1 , prupe-m5vl29 , prupe-m5vn82 , prupe-m5vq88 , prupe-m5y2s7 , prupe-m5wye7 , prupe-m5wxm4 , prupe-m5xqp6 , prupe-m5x4q4 , prupe-m5x4m1 , prupe-m5x6b3 , prupe-m5vlb6 , prupe-m5w4h3 , prupe-m5vlu4 , prupe-m5vln3 , prupe-a0a251myy7 , prupe-a0a251mws4 , prupe-m5vi18 , prupe-m5vh66 , prupe-m5xd54 , prupe-m5xqn2 , prupe-m5xr64 , prupe-m5vrm7 , prupe-m5vrk6 , prupe-m5vqp6 , prupe-a0a251nbb1 , prupe-a0a251nbd3 , prupe-a0a251nbb3 , prupe-a0a251nba0 , prupe-a0a251ndd4 , prupe-a0a251nbb6 , prupe-m5w315 , prupe-a0a251mwh1 , prupe-a0a251qn57 , prupe-m5vzh8 , prupe-m5xpz7 , prupe-m5xrp5 , prupe-m5wsr5 , prupe-m5xs20 , prupe-m5vl10 , prupe-a0a251nay9 , prupe-a0a251ndz1 , prupe-a0a251puf0 , prupe-m5wr61 , prupe-a0a251nyu6 , prupe-m5vl63

Title : The genome of melon (Cucumis melo L.) - Garcia-Mas_2012_Proc.Natl.Acad.Sci.U.S.A_109_11872
Author(s) : Garcia-Mas J , Benjak A , Sanseverino W , Bourgeois M , Mir G , Gonzalez VM , Henaff E , Camara F , Cozzuto L , Lowy E , Alioto T , Capella-Gutierrez S , Blanca J , Canizares J , Ziarsolo P , Gonzalez-Ibeas D , Rodriguez-Moreno L , Droege M , Du L , Alvarez-Tejado M , Lorente-Galdos B , Mele M , Yang L , Weng Y , Navarro A , Marques-Bonet T , Aranda MA , Nuez F , Pico B , Gabaldon T , Roma G , Guigo R , Casacuberta JM , Arus P , Puigdomenech P
Ref : Proc Natl Acad Sci U S A , 109 :11872 , 2012
Abstract : We report the genome sequence of melon, an important horticultural crop worldwide. We assembled 375 Mb of the double-haploid line DHL92, representing 83.3% of the estimated melon genome. We predicted 27,427 protein-coding genes, which we analyzed by reconstructing 22,218 phylogenetic trees, allowing mapping of the orthology and paralogy relationships of sequenced plant genomes. We observed the absence of recent whole-genome duplications in the melon lineage since the ancient eudicot triplication, and our data suggest that transposon amplification may in part explain the increased size of the melon genome compared with the close relative cucumber. A low number of nucleotide-binding site-leucine-rich repeat disease resistance genes were annotated, suggesting the existence of specific defense mechanisms in this species. The DHL92 genome was compared with that of its parental lines allowing the quantification of sequence variability in the species. The use of the genome sequence in future investigations will facilitate the understanding of evolution of cucurbits and the improvement of breeding strategies.
ESTHER : Garcia-Mas_2012_Proc.Natl.Acad.Sci.U.S.A_109_11872
PubMedSearch : Garcia-Mas_2012_Proc.Natl.Acad.Sci.U.S.A_109_11872
PubMedID: 22753475
Gene_locus related to this paper: cucme-a0a1s3cge4 , cucme-a0a1s3ct47 , cucme-a0a1s3bcl7 , cucsa-a0a0a0m228 , cucme-a0a1s3bnl4 , cucme-a0a1s3b1c9 , cucme-a0a1s3b1d4 , cucme-a0a1s3buy0 , cucme-a0a1s3bva9 , cucme-a0a1s3c6j4 , cucme-a0a1s3cky2 , cucme-a0a1s3clz8 , cucme-a0a1s3buy6 , cucme-a0a1s3bp26

Title : Generation of a BAC-based physical map of the melon genome - Gonzalez_2010_BMC.Genomics_11_339
Author(s) : Gonzalez VM , Garcia-Mas J , Arus P , Puigdomenech P
Ref : BMC Genomics , 11 :339 , 2010
Abstract : BACKGROUND: Cucumis melo (melon) belongs to the Cucurbitaceae family, whose economic importance among horticulture crops is second only to Solanaceae. Melon has high intra-specific genetic variation, morphologic diversity and a small genome size (450 Mb), which make this species suitable for a great variety of molecular and genetic studies that can lead to the development of tools for breeding varieties of the species. A number of genetic and genomic resources have already been developed, such as several genetic maps and BAC genomic libraries. These tools are essential for the construction of a physical map, a valuable resource for map-based cloning, comparative genomics and assembly of whole genome sequencing data. However, no physical map of any Cucurbitaceae has yet been developed. A project has recently been started to sequence the complete melon genome following a whole-genome shotgun strategy, which makes use of massive sequencing data. A BAC-based melon physical map will be a useful tool to help assemble and refine the draft genome data that is being produced.
RESULTS: A melon physical map was constructed using a 5.7 x BAC library and a genetic map previously developed in our laboratories. High-information-content fingerprinting (HICF) was carried out on 23,040 BAC clones, digesting with five restriction enzymes and SNaPshot labeling, followed by contig assembly with FPC software. The physical map has 1,355 contigs and 441 singletons, with an estimated physical length of 407 Mb (0.9 x coverage of the genome) and the longest contig being 3.2 Mb. The anchoring of 845 BAC clones to 178 genetic markers (100 RFLPs, 76 SNPs and 2 SSRs) also allowed the genetic positioning of 183 physical map contigs/singletons, representing 55 Mb (12%) of the melon genome, to individual chromosomal loci. The melon FPC database is available for download at http:\/\/
CONCLUSIONS: Here we report the construction of the first physical map of a Cucurbitaceae species described so far. The physical map was integrated with the genetic map so that a number of physical contigs, representing 12% of the melon genome, could be anchored to known genetic positions. The data presented is already helping to improve the quality of the melon genomic sequence available as a result of a project currently being carried out in Spain, adopting a whole genome shotgun approach based on 454 sequencing data.
ESTHER : Gonzalez_2010_BMC.Genomics_11_339
PubMedSearch : Gonzalez_2010_BMC.Genomics_11_339
PubMedID: 20509895

Title : Structure of two melon regions reveals high microsynteny with sequenced plant species - Deleu_2007_Mol.Genet.Genomics_278_611
Author(s) : Deleu W , Gonzalez V , Monfort A , Bendahmane A , Puigdomenech P , Arus P , Garcia-Mas J
Ref : Mol Genet Genomics , 278 :611 , 2007
Abstract : In this study, two melon bacterial artificial chromosome (BAC) clones have been sequenced and annotated. BAC 1-21-10 spans 92 kb and contains the nsv locus conferring resistance to the Melon Necrotic Spot Virus (MNSV) in melon linkage group 11. BAC 13J4 spans 98 kb and belongs to a BAC contig containing resistance gene homologues, extending a previous sequenced region of 117 kb in linkage group 4. Both regions have microsyntenic relationships to the model plant species Arabidopsis thaliana, and to Medicago truncatula and Populus trichocarpa. The network of synteny found between melon and each of the sequenced genomes reflects the polyploid structure of Arabidopsis, Populus, and Medicago genomes due to whole genome duplications (WGD). A detailed analysis revealed that both melon regions have a lower relative syntenic quality with Arabidopsis (eurosid II) than when compared to Populus and Medicago (eurosid I). Although phylogenetically Cucurbitales seem to be closer to Fabales than to Malphigiales, synteny was higher between both melon regions and Populus. Presented data imply that the recently completed Populus genome sequence could preferentially be used to obtain positional information in melon, based on microsynteny.
ESTHER : Deleu_2007_Mol.Genet.Genomics_278_611
PubMedSearch : Deleu_2007_Mol.Genet.Genomics_278_611
PubMedID: 17665215