Salse J

References (6)

Title : High-quality genome sequence of white lupin provides insight into soil exploration and seed quality - Hufnagel_2020_Nat.Commun_11_492
Author(s) : Hufnagel B , Marques A , Soriano A , Marques L , Divol F , Doumas P , Sallet E , Mancinotti D , Carrere S , Marande W , Arribat S , Keller J , Huneau C , Blein T , Aime D , Laguerre M , Taylor J , Schubert V , Nelson M , Geu-Flores F , Crespi M , Gallardo K , Delaux PM , Salse J , Berges H , Guyot R , Gouzy J , Peret B
Ref : Nat Commun , 11 :492 , 2020
Abstract : White lupin (Lupinus albus L.) is an annual crop cultivated for its protein-rich seeds. It is adapted to poor soils due to the production of cluster roots, which are made of dozens of determinate lateral roots that drastically improve soil exploration and nutrient acquisition (mostly phosphate). Using long-read sequencing technologies, we provide a high-quality genome sequence of a cultivated accession of white lupin (2n = 50, 451 Mb), as well as de novo assemblies of a landrace and a wild relative. We describe a modern accession displaying increased soil exploration capacity through early establishment of lateral and cluster roots. We also show how seed quality may have been impacted by domestication in term of protein profiles and alkaloid content. The availability of a high-quality genome assembly together with companion genomic and transcriptomic resources will enable the development of modern breeding strategies to increase and stabilize white lupin yield.
ESTHER : Hufnagel_2020_Nat.Commun_11_492
PubMedSearch : Hufnagel_2020_Nat.Commun_11_492
PubMedID: 31980615
Gene_locus related to this paper: lupal-a0a6a5lz53 , lupal-a0a6a5mjk3

Title : The Rosa genome provides new insights into the domestication of modern roses - Raymond_2018_Nat.Genet_50_772
Author(s) : Raymond O , Gouzy J , Just J , Badouin H , Verdenaud M , Lemainque A , Vergne P , Moja S , Choisne N , Pont C , Carrere S , Caissard JC , Couloux A , Cottret L , Aury JM , Szecsi J , Latrasse D , Madoui MA , Francois L , Fu X , Yang SH , Dubois A , Piola F , Larrieu A , Perez M , Labadie K , Perrier L , Govetto B , Labrousse Y , Villand P , Bardoux C , Boltz V , Lopez-Roques C , Heitzler P , Vernoux T , Vandenbussche M , Quesneville H , Boualem A , Bendahmane A , Liu C , Le Bris M , Salse J , Baudino S , Benhamed M , Wincker P , Bendahmane M
Ref : Nat Genet , 50 :772 , 2018
Abstract : Roses have high cultural and economic importance as ornamental plants and in the perfume industry. We report the rose whole-genome sequencing and assembly and resequencing of major genotypes that contributed to rose domestication. We generated a homozygous genotype from a heterozygous diploid modern rose progenitor, Rosa chinensis 'Old Blush'. Using single-molecule real-time sequencing and a meta-assembly approach, we obtained one of the most comprehensive plant genomes to date. Diversity analyses highlighted the mosaic origin of 'La France', one of the first hybrids combining the growth vigor of European species and the recurrent blooming of Chinese species. Genomic segments of Chinese ancestry identified new candidate genes for recurrent blooming. Reconstructing regulatory and secondary metabolism pathways allowed us to propose a model of interconnected regulation of scent and flower color. This genome provides a foundation for understanding the mechanisms governing rose traits and should accelerate improvement in roses, Rosaceae and ornamentals.
ESTHER : Raymond_2018_Nat.Genet_50_772
PubMedSearch : Raymond_2018_Nat.Genet_50_772
PubMedID: 29713014
Gene_locus related to this paper: rosch-a0a2p6p237 , rosch-a0a2p6r1h5 , rosch-a0a2p6saq0 , rosch-a0a2p6sap4 , rosch-a0a2p6san0 , rosch-a0a2p6san7 , rosch-a0a2p6rkg2 , rosch-a0a2p6pxu1 , rosch-a0a2p6s382 , rosch-a0a2p6s367 , rosch-a0a2p6q0b7 , rosch-a0a2p6pi87 , rosch-a0a2p6p278 , rosch-a0a2p6s545 , rosch-a0a2p6r6x5 , rosch-a0a2p6rqc2

Title : The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution - Lang_2018_Plant.J_93_515
Author(s) : Lang D , Ullrich KK , Murat F , Fuchs J , Jenkins J , Haas FB , Piednoel M , Gundlach H , Van Bel M , Meyberg R , Vives C , Morata J , Symeonidi A , Hiss M , Muchero W , Kamisugi Y , Saleh O , Blanc G , Decker EL , van Gessel N , Grimwood J , Hayes RD , Graham SW , Gunter LE , McDaniel SF , Hoernstein SNW , Larsson A , Li FW , Perroud PF , Phillips J , Ranjan P , Rokshar DS , Rothfels CJ , Schneider L , Shu S , Stevenson DW , Thummler F , Tillich M , Villarreal Aguilar JC , Widiez T , Wong GK , Wymore A , Zhang Y , Zimmer AD , Quatrano RS , Mayer KFX , Goodstein D , Casacuberta JM , Vandepoele K , Reski R , Cuming AC , Tuskan GA , Maumus F , Salse J , Schmutz J , Rensing SA
Ref : Plant J , 93 :515 , 2018
Abstract : The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene- and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.
ESTHER : Lang_2018_Plant.J_93_515
PubMedSearch : Lang_2018_Plant.J_93_515
PubMedID: 29237241
Gene_locus related to this paper: phypa-a9tc36 , phypa-a0a2k1kfe3 , phypa-a9sqk3 , phypa-a0a2k1ie71 , phypa-a0a2k1kg29 , phypa-a0a2k1iji3

Title : The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution - Badouin_2017_Nature_546_148
Author(s) : Badouin H , Gouzy J , Grassa CJ , Murat F , Staton SE , Cottret L , Lelandais-Briere C , Owens GL , Carrere S , Mayjonade B , Legrand L , Gill N , Kane NC , Bowers JE , Hubner S , Bellec A , Berard A , Berges H , Blanchet N , Boniface MC , Brunel D , Catrice O , Chaidir N , Claudel C , Donnadieu C , Faraut T , Fievet G , Helmstetter N , King M , Knapp SJ , Lai Z , Le Paslier MC , Lippi Y , Lorenzon L , Mandel JR , Marage G , Marchand G , Marquand E , Bret-Mestries E , Morien E , Nambeesan S , Nguyen T , Pegot-Espagnet P , Pouilly N , Raftis F , Sallet E , Schiex T , Thomas J , Vandecasteele C , Vares D , Vear F , Vautrin S , Crespi M , Mangin B , Burke JM , Salse J , Munos S , Vincourt P , Rieseberg LH , Langlade NB
Ref : Nature , 546 :148 , 2017
Abstract : The domesticated sunflower, Helianthus annuus L., is a global oil crop that has promise for climate change adaptation, because it can maintain stable yields across a wide variety of environmental conditions, including drought. Even greater resilience is achievable through the mining of resistance alleles from compatible wild sunflower relatives, including numerous extremophile species. Here we report a high-quality reference for the sunflower genome (3.6 gigabases), together with extensive transcriptomic data from vegetative and floral organs. The genome mostly consists of highly similar, related sequences and required single-molecule real-time sequencing technologies for successful assembly. Genome analyses enabled the reconstruction of the evolutionary history of the Asterids, further establishing the existence of a whole-genome triplication at the base of the Asterids II clade and a sunflower-specific whole-genome duplication around 29 million years ago. An integrative approach combining quantitative genetics, expression and diversity data permitted development of comprehensive gene networks for two major breeding traits, flowering time and oil metabolism, and revealed new candidate genes in these networks. We found that the genomic architecture of flowering time has been shaped by the most recent whole-genome duplication, which suggests that ancient paralogues can remain in the same regulatory networks for dozens of millions of years. This genome represents a cornerstone for future research programs aiming to exploit genetic diversity to improve biotic and abiotic stress resistance and oil production, while also considering agricultural constraints and human nutritional needs.
ESTHER : Badouin_2017_Nature_546_148
PubMedSearch : Badouin_2017_Nature_546_148
PubMedID: 28538728
Gene_locus related to this paper: helan-a0a251rty5 , helan-a0a251rwi0 , helan-a0a251s4p0 , helan-a0a251tv75 , helan-a0a251s253 , helan-a0a251ts58 , helan-a0a251vmq8 , helan-a0a251rur6 , helan-a0a251ve88 , helan-a0a251rzb7 , helan-a0a251uh88 , helan-a0a251ux90 , helan-a0a251sb83 , helan-a0a251txv8 , helan-a0a251u1d0 , helan-a0a251uwi4 , helan-a0a251uwk5 , helan-a0a251uxe9 , helan-a0a251vi64

Title : The genome of Eucalyptus grandis - Myburg_2014_Nature_510_356
Author(s) : Myburg AA , Grattapaglia D , Tuskan GA , Hellsten U , Hayes RD , Grimwood J , Jenkins J , Lindquist E , Tice H , Bauer D , Goodstein DM , Dubchak I , Poliakov A , Mizrachi E , Kullan AR , Hussey SG , Pinard D , van der Merwe K , Singh P , van Jaarsveld I , Silva-Junior OB , Togawa RC , Pappas MR , Faria DA , Sansaloni CP , Petroli CD , Yang X , Ranjan P , Tschaplinski TJ , Ye CY , Li T , Sterck L , Vanneste K , Murat F , Soler M , Clemente HS , Saidi N , Cassan-Wang H , Dunand C , Hefer CA , Bornberg-Bauer E , Kersting AR , Vining K , Amarasinghe V , Ranik M , Naithani S , Elser J , Boyd AE , Liston A , Spatafora JW , Dharmwardhana P , Raja R , Sullivan C , Romanel E , Alves-Ferreira M , Kulheim C , Foley W , Carocha V , Paiva J , Kudrna D , Brommonschenkel SH , Pasquali G , Byrne M , Rigault P , Tibbits J , Spokevicius A , Jones RC , Steane DA , Vaillancourt RE , Potts BM , Joubert F , Barry K , Pappas GJ , Strauss SH , Jaiswal P , Grima-Pettenati J , Salse J , Van de Peer Y , Rokhsar DS , Schmutz J
Ref : Nature , 510 :356 , 2014
Abstract : Eucalypts are the world's most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled >94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes. Eucalyptus also shows the highest diversity of genes for specialized metabolites such as terpenes that act as chemical defence and provide unique pharmaceutical oils. Genome sequencing of the E. grandis sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression. The E. grandis genome is the first reference for the eudicot order Myrtales and is placed here sister to the eurosids. This resource expands our understanding of the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.
ESTHER : Myburg_2014_Nature_510_356
PubMedSearch : Myburg_2014_Nature_510_356
PubMedID: 24919147
Gene_locus related to this paper: eucgr-a0a059d0n8 , eucgr-a0a059cm68 , eucgr-a0a059d783 , eucgr-a0a059af93 , eucgr-a0a059awi0 , eucgr-a0a059awt4 , eucgr-a0a059ar83 , eucgr-a0a059ayw5 , eucgr-a0a059az75 , eucgr-a0a059azj1 , eucgr-a0a059azq5 , eucgr-a0a059bkm2 , eucgr-a0a059bl38 , eucgr-a0a059a7m2 , eucgr-a0a059a6p6 , eucgr-a0a059a6p1 , eucgr-a0a059a5e9 , eucgr-a0a059cpq4 , eucgr-a0a059b8v5

Title : Genome sequencing and analysis of the model grass Brachypodium distachyon. -
Author(s) : Vogel JP , Garvin DF , Mockler TC , Schmutz J , Rokhsar D , Bevan MW , Barry K , Lucas S , Harmon-Smith M , Lail K , Tice H , Grimwood J , McKenzie N , Huo N , Gu YQ , Lazo GR , Anderson OD , You FM , Luo MC , Dvorak J , Wright J , Febrer M , Idziak D , Hasterok R , Lindquist E , Wang M , Fox SE , Priest HD , Filichkin SA , Givan SA , Bryant DW , Chang JH , Wu H , Wu W , Hsia AP , Schnable PS , Kalyanaraman A , Barbazuk B , Michael TP , Hazen SP , Bragg JN , Laudencia-Chingcuanco D , Weng Y , Haberer G , Spannagl M , Mayer K , Rattei T , Mitros T , Lee SJ , Rose JK , Mueller LA , York TL , Wicker T , Buchmann JP , Tanskanen J , Schulman AH , Gundlach H , Bevan M , de Oliveira AC , Maia Lda C , Belknap W , Jiang N , Lai J , Zhu L , Ma J , Sun C , Pritham E , Salse J , Murat F , Abrouk M , Bruggmann R , Messing J , Fahlgren N , Sullivan CM , Carrington JC , Chapman EJ , May GD , Zhai J , Ganssmann M , Gurazada SG , German M , Meyers BC , Green PJ , Tyler L , Wu J , Thomson J , Chen S , Scheller HV , Harholt J , Ulvskov P , Kimbrel JA , Bartley LE , Cao P , Jung KH , Sharma MK , Vega-Sanchez M , Ronald P , Dardick CD , De Bodt S , Verelst W , Inz D , Heese M , Schnittger A , Yang X , Kalluri UC , Tuskan GA , Hua Z , Vierstra RD , Cui Y , Ouyang S , Sun Q , Liu Z , Yilmaz A , Grotewold E , Sibout R , Hematy K , Mouille G , Hofte H , Michael T , Pelloux J , O'Connor D , Schnable J , Rowe S , Harmon F , Cass CL , Sedbrook JC , Byrne ME , Walsh S , Higgins J , Li P , Brutnell T , Unver T , Budak H , Belcram H , Charles M , Chalhoub B , Baxter I
Ref : Nature , 463 :763 , 2010
PubMedID: 20148030
Gene_locus related to this paper: bradi-i1grm0 , bradi-i1gx82 , bradi-i1hb80 , bradi-i1hkv6 , bradi-i1hpu6 , bradi-i1i3e4 , bradi-i1i9i0 , bradi-i1i435 , bradi-i1ix93 , bradi-i1gsk6 , bradi-i1hk44 , bradi-i1hk45 , bradi-i1hnk7 , bradi-i1hsd5 , bradi-i1huy4 , bradi-i1huy9 , bradi-i1huz0 , bradi-i1gxx9 , bradi-i1hl25 , bradi-i1hcw7 , bradi-i1hyv6 , bradi-i1hyb5 , bradi-i1hvr8 , bradi-i1hmu2 , bradi-i1hf05 , bradi-i1gry7 , bradi-i1hf06 , bradi-i1i5z8 , bradi-i1icy3 , bradi-i1j1h3 , bradi-i1h1e3 , bradi-i1hvr9 , bradi-a0a0q3r7i7 , bradi-i1i377 , bradi-i1hjg5 , bradi-i1h3i9 , bradi-i1gsg5 , bradi-a0a0q3mph9 , bradi-i1h682 , bradi-a0a0q3lc91 , bradi-i1gx49 , bradi-i1i839 , bradi-a0a2k2dsp5 , bradi-i1gsb5