Berard A

References (3)

Title : Whole-genome landscape of Medicago truncatula symbiotic genes - Pecrix_2018_Nat.Plants_4_1017
Author(s) : Pecrix Y , Staton SE , Sallet E , Lelandais-Briere C , Moreau S , Carrere S , Blein T , Jardinaud MF , Latrasse D , Zouine M , Zahm M , Kreplak J , Mayjonade B , Satge C , Perez M , Cauet S , Marande W , Chantry-Darmon C , Lopez-Roques C , Bouchez O , Berard A , Debelle F , Munos S , Bendahmane A , Berges H , Niebel A , Buitink J , Frugier F , Benhamed M , Crespi M , Gouzy J , Gamas P
Ref : Nat Plants , 4 :1017 , 2018
Abstract : Advances in deciphering the functional architecture of eukaryotic genomes have been facilitated by recent breakthroughs in sequencing technologies, enabling a more comprehensive representation of genes and repeat elements in genome sequence assemblies, as well as more sensitive and tissue-specific analyses of gene expression. Here we show that PacBio sequencing has led to a substantially improved genome assembly of Medicago truncatula A17, a legume model species notable for endosymbiosis studies(1), and has enabled the identification of genome rearrangements between genotypes at a near-base-pair resolution. Annotation of the new M. truncatula genome sequence has allowed for a thorough analysis of transposable elements and their dynamics, as well as the identification of new players involved in symbiotic nodule development, in particular 1,037 upregulated long non-coding RNAs (lncRNAs). We have also discovered that a substantial proportion (~35% and 38%, respectively) of the genes upregulated in nodules or expressed in the nodule differentiation zone colocalize in genomic clusters (270 and 211, respectively), here termed symbiotic islands. These islands contain numerous expressed lncRNA genes and display differentially both DNA methylation and histone marks. Epigenetic regulations and lncRNAs are therefore attractive candidate elements for the orchestration of symbiotic gene expression in the M. truncatula genome.
ESTHER : Pecrix_2018_Nat.Plants_4_1017
PubMedSearch : Pecrix_2018_Nat.Plants_4_1017
PubMedID: 30397259
Gene_locus related to this paper: medtr-q1s5d8 , medtr-q1t171 , medtr-g7kmk5 , medtr-a0a072uuf6 , medtr-a0a072urp3 , medtr-g7zzc3 , medtr-a0a072u5k5 , medtr-a0a072v056 , medtr-scp1 , medtr-g7kyn0 , medtr-g7inw6 , medtr-g7j3q3

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 : Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome - Chalhoub_2014_Science_345_950
Author(s) : Chalhoub B , Denoeud F , Liu S , Parkin IA , Tang H , Wang X , Chiquet J , Belcram H , Tong C , Samans B , Correa M , Da Silva C , Just J , Falentin C , Koh CS , Le Clainche I , Bernard M , Bento P , Noel B , Labadie K , Alberti A , Charles M , Arnaud D , Guo H , Daviaud C , Alamery S , Jabbari K , Zhao M , Edger PP , Chelaifa H , Tack D , Lassalle G , Mestiri I , Schnel N , Le Paslier MC , Fan G , Renault V , Bayer PE , Golicz AA , Manoli S , Lee TH , Thi VH , Chalabi S , Hu Q , Fan C , Tollenaere R , Lu Y , Battail C , Shen J , Sidebottom CH , Canaguier A , Chauveau A , Berard A , Deniot G , Guan M , Liu Z , Sun F , Lim YP , Lyons E , Town CD , Bancroft I , Meng J , Ma J , Pires JC , King GJ , Brunel D , Delourme R , Renard M , Aury JM , Adams KL , Batley J , Snowdon RJ , Tost J , Edwards D , Zhou Y , Hua W , Sharpe AG , Paterson AH , Guan C , Wincker P
Ref : Science , 345 :950 , 2014
Abstract : Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72x genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.
ESTHER : Chalhoub_2014_Science_345_950
PubMedSearch : Chalhoub_2014_Science_345_950
PubMedID: 25146293
Gene_locus related to this paper: braol-Q8GTM3 , braol-Q8GTM4 , brana-a0a078j4a9 , brana-a0a078e1m0 , brana-a0a078cd75 , brana-a0a078evd3 , brana-a0a078j4f0 , brana-a0a078cta5 , brana-a0a078cus4 , brana-a0a078f8c2 , brana-a0a078jql1 , brana-a0a078dgj3 , brana-a0a078hw50 , brana-a0a078cuu0 , brana-a0a078iyl8 , brana-a0a078dfa9 , brana-a0a078ic91 , brana-a0a078cnf7 , brana-a0a078fh41 , brana-a0a078ca65 , brana-a0a078ctc8 , brana-a0a078h021 , brana-a0a078h0h8 , brana-a0a078jx23 , brana-a0a078ci96 , brana-a0a078cqd7 , brana-a0a078dh94 , brana-a0a078h612 , brana-a0a078ild2 , brana-a0a078j2t3 , braol-a0a0d3dpb2 , braol-a0a0d3dx76 , brana-a0a078jxa8 , brana-a0a078i2k3 , braol-a0a0d3ef55 , brarp-m4dcj8 , brana-a0a078fw53 , brana-a0a078itf3 , brana-a0a078jsn1 , brana-a0a078jrt9 , brana-a0a078i6d2 , brana-a0a078jku0 , brana-a0a078fss7 , brana-a0a078i1l0 , brana-a0a078i402