ALBERT

Description: Plant genomes, and eukaryotic genomes in general, are typically repetitive, polyploid and heterozygous, which complicates genome assembly. The short read lengths of early Sanger and current next-generation sequencing platforms hinder assembly through complex repeat regions, and many draft and reference genomes are fragmented, lacking skewed GC and repetitive intergenic sequences, which are gaining importance due to projects like the Encyclopedia of DNA Elements (ENCODE). Here we report the whole-genome sequencing and assembly of the desiccation-tolerant grass Oropetium thomaeum. Using only single-molecule real-time sequencing, which generates long (〉16 kilobases) reads with random errors, we assembled 99% (244 megabases) of the Oropetium genome into 625 contigs with an N50 length of 2.4 megabases. Oropetium is an example of a 'near-complete' draft genome which includes gapless coverage over gene space as well as intergenic sequences such as centromeres, telomeres, transposable elements and rRNA clusters that are typically unassembled in draft genomes. Oropetium has 28,466 protein-coding genes and 43% repeat sequences, yet with 30% more compact euchromatic regions it is the smallest known grass genome. The Oropetium genome demonstrates the utility of single-molecule real-time sequencing for assembling high-quality plant and other eukaryotic genomes, and serves as a valuable resource for the plant comparative genomics community.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉VanBuren, Robert -- Bryant, Doug -- Edger, Patrick P -- Tang, Haibao -- Burgess, Diane -- Challabathula, Dinakar -- Spittle, Kristi -- Hall, Richard -- Gu, Jenny -- Lyons, Eric -- Freeling, Michael -- Bartels, Dorothea -- Ten Hallers, Boudewijn -- Hastie, Alex -- Michael, Todd P -- Mockler, Todd C -- England -- Nature. 2015 Nov 26;527(7579):508-11. doi: 10.1038/nature15714. Epub 2015 Nov 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA. ; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720, USA. ; Department of Horticulture, Michigan State University, East Lansing, Michigan 48823, USA. ; iPlant Collaborative, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA. ; Center for Genomics and Biotechnology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou 350002, China. ; IMBIO, University of Bonn, Kirschallee 1, D-53115 Bonn, Germany. ; Pacific Biosciences, Menlo Park, California 94025, USA. ; BioNano Genomics, San Diego, California 92121, USA. ; Ibis Biosciences, Carlsbad, California 92008, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26560029" target="_blank"〉PubMed〈/a〉

Description: 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.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chalhoub, Boulos -- Denoeud, France -- Liu, Shengyi -- Parkin, Isobel A P -- Tang, Haibao -- Wang, Xiyin -- Chiquet, Julien -- Belcram, Harry -- Tong, Chaobo -- Samans, Birgit -- Correa, Margot -- Da Silva, Corinne -- Just, Jeremy -- Falentin, Cyril -- Koh, Chu Shin -- Le Clainche, Isabelle -- Bernard, Maria -- Bento, Pascal -- Noel, Benjamin -- Labadie, Karine -- Alberti, Adriana -- Charles, Mathieu -- Arnaud, Dominique -- Guo, Hui -- Daviaud, Christian -- Alamery, Salman -- Jabbari, Kamel -- Zhao, Meixia -- Edger, Patrick P -- Chelaifa, Houda -- Tack, David -- Lassalle, Gilles -- Mestiri, Imen -- Schnel, Nicolas -- Le Paslier, Marie-Christine -- Fan, Guangyi -- Renault, Victor -- Bayer, Philippe E -- Golicz, Agnieszka A -- Manoli, Sahana -- Lee, Tae-Ho -- Thi, Vinh Ha Dinh -- Chalabi, Smahane -- Hu, Qiong -- Fan, Chuchuan -- Tollenaere, Reece -- Lu, Yunhai -- Battail, Christophe -- Shen, Jinxiong -- Sidebottom, Christine H D -- Wang, Xinfa -- Canaguier, Aurelie -- Chauveau, Aurelie -- Berard, Aurelie -- Deniot, Gwenaelle -- Guan, Mei -- Liu, Zhongsong -- Sun, Fengming -- Lim, Yong Pyo -- Lyons, Eric -- Town, Christopher D -- Bancroft, Ian -- Wang, Xiaowu -- Meng, Jinling -- Ma, Jianxin -- Pires, J Chris -- King, Graham J -- Brunel, Dominique -- Delourme, Regine -- Renard, Michel -- Aury, Jean-Marc -- Adams, Keith L -- Batley, Jacqueline -- Snowdon, Rod J -- Tost, Jorg -- Edwards, David -- Zhou, Yongming -- Hua, Wei -- Sharpe, Andrew G -- Paterson, Andrew H -- Guan, Chunyun -- Wincker, Patrick -- BB/E017363/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2014 Aug 22;345(6199):950-3. doi: 10.1126/science.1253435. Epub 2014 Aug 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut National de Recherche Agronomique (INRA)/Universite d'Evry Val d'Essone, Unite de Recherche en Genomique Vegetale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Cremieux, 91057 Evry, France. chalhoub@evry.inra.fr. ; Commissariat a l'Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, BP5706, 91057 Evry, France. Universite d'Evry Val d'Essone, UMR 8030, CP5706, Evry, France. Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706, Evry, France. ; Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China. ; Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada. chalhoub@evry.inra.fr. ; J. Craig Venter Institute, Rockville, MD 20850, USA. Center for Genomics and Biotechnology, Fujian Agriculture and Forestry, University, Fuzhou 350002, Fujian Province, China. ; Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA. Center of Genomics and Computational Biology, School of Life Sciences, Hebei United University, Tangshan, Hebei 063000, China. ; Laboratoire de Mathematiques et Modelisation d'Evry-UMR 8071 CNRS/Universite d'Evry val d'Essonne-USC INRA, Evry, France. ; Institut National de Recherche Agronomique (INRA)/Universite d'Evry Val d'Essone, Unite de Recherche en Genomique Vegetale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Cremieux, 91057 Evry, France. ; Department of Plant Breeding, Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany. ; Commissariat a l'Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, BP5706, 91057 Evry, France. ; INRA, Institut de Genetique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France. ; National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada. ; INRA, Etude du Polymorphisme des Genomes Vegetaux, US1279, Centre National de Genotypage, CEA-IG, 2 rue Gaston Cremieux, 91057 Evry, France. ; Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA. ; Laboratory for Epigenetics and Environment, Centre National de Genotypage, CEA-IG, 2 rue Gaston Cremieux, 91000 Evry, France. ; Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia. ; Institut National de Recherche Agronomique (INRA)/Universite d'Evry Val d'Essone, Unite de Recherche en Genomique Vegetale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Cremieux, 91057 Evry, France. Cologne Center for Genomics, University of Cologne, Weyertal 115b, 50931 Koln, Germany. ; Department of Agronomy, Purdue University, WSLR Building B018, West Lafayette, IN 47907, USA. ; Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA. ; Department of Botany, University of British Columbia, Vancouver, BC, Canada. ; Beijing Genome Institute-Shenzhen, Shenzhen 518083, China. ; Fondation Jean Dausset-Centre d'Etude du Polymorphisme Humain, 27 rue Juliette Dodu, 75010 Paris, France. ; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China. ; College of Agronomy, Hunan Agricultural University, Changsha 410128, China. ; Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon-305764, South Korea. ; School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, AZ, USA. ; J. Craig Venter Institute, Rockville, MD 20850, USA. ; Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK. ; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China. ; Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA. ; Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia. ; Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia. School of Plant Biology, University of Western Australia, WA 6009, Australia. ; Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia. School of Plant Biology, University of Western Australia, WA 6009, Australia. chalhoub@evry.inra.fr. ; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China. chalhoub@evry.inra.fr. ; Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China. chalhoub@evry.inra.fr. ; National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada. chalhoub@evry.inra.fr. ; Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA. chalhoub@evry.inra.fr. ; College of Agronomy, Hunan Agricultural University, Changsha 410128, China. chalhoub@evry.inra.fr. ; Commissariat a l'Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, BP5706, 91057 Evry, France. Universite d'Evry Val d'Essone, UMR 8030, CP5706, Evry, France. Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706, Evry, France. chalhoub@evry.inra.fr.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25146293" target="_blank"〉PubMed〈/a〉

Description: Coevolutionary interactions are thought to have spurred the evolution of key innovations and driven the diversification of much of life on Earth. However, the genetic and evolutionary basis of the innovations that facilitate such interactions remains poorly understood. We examined the coevolutionary interactions between plants (Brassicales) and butterflies (Pieridae), and...

Description: Brassicaceae is one of the most diverse and economically valuable angiosperm families with widely cultivated vegetable crops and scientifically important model plants, such as Arabidopsis thaliana . The evolutionary history, ecological, morphological, and genetic diversity, and abundant resources and knowledge of Brassicaceae make it an excellent model family for evolutionary studies. Recent phylogenetic analyses of the family revealed three major lineages (I, II, and III), but relationships among and within these lineages remain largely unclear. Here, we present a highly supported phylogeny with six major clades using nuclear markers from newly sequenced transcriptomes of 32 Brassicaceae species and large data sets from additional taxa for a total of 55 species spanning 29 out of 51 tribes. Clade A consisting of Lineage I and Macropodium nivale is sister to combined Clade B (with Lineage II and others) and a new Clade C. The ABC clade is sister to Clade D with species previously weakly associated with Lineage II and Clade E (Lineage III) is sister to the ABCD clade. Clade F (the tribe Aethionemeae) is sister to the remainder of the entire family. Molecular clock estimation reveals an early radiation of major clades near or shortly after the Eocene–Oligocene boundary and subsequent nested divergences of several tribes of the previously polytomous Expanded Lineage II. Reconstruction of ancestral morphological states during the Brassicaceae evolution indicates prevalent parallel (convergent) evolution of several traits over deep times across the entire family. These results form a foundation for future evolutionary analyses of structures and functions across Brassicaceae.

Description: Plants share a common history of successive whole-genome duplication (WGD) events retaining genomic patterns of duplicate gene copies (ohnologs) organized in conserved syntenic blocks. Duplication was often proposed to affect the origin of novel traits during evolution. However, genetic evidence linking WGD to pathway diversification is scarce. We show that WGD and tandem duplication (TD) accelerated genetic versatility of plant secondary metabolism, exemplified with the glucosinolate (GS) pathway in the mustard family. GS biosynthesis is a well-studied trait, employing at least 52 biosynthetic and regulatory genes in the model plant Arabidopsis. In a phylogenomics approach, we identified 67 GS loci in Aethionema arabicum of the tribe Aethionemae, sister group to all mustard family members. All but one of the Arabidopsis GS gene families evolved orthologs in Aethionema and all but one of the orthologous sequence pairs exhibit synteny . The 45% fraction of duplicates among all protein-coding genes in Arabidopsis was increased to 95% and 97% for Arabidopsis and Aethionema GS pathway inventory, respectively. Compared with the 22% average for all protein-coding genes in Arabidopsis, 52% and 56% of Aethionema and Arabidopsis GS loci align to ohnolog copies dating back to the last common WGD event. Although 15% of all Arabidopsis genes are organized in tandem arrays, 45% and 48% of GS loci in Arabidopsis and Aethionema descend from TD, respectively. We describe a sequential combination of TD and WGD events driving gene family extension, thereby expanding the evolutionary playground for functional diversification and thus potential novelty and success.

Description: Fusarium wilt, a soil-borne disease caused by the fungal pathogen Fusarium oxysporum f. sp. fragariae , threatens strawberry ( Fragaria x ananassa ) production worldwide. The spread of the pathogen, coupled with disruptive changes in soil fumigation practices, have greatly increased disease pressure and the importance of developing resistant cultivars. While resistant and susceptible cultivars have been reported, a limited number of germplasm accessions have been analyzed, and contradictory conclusions have been reached in earlier studies to elucidate the underlying genetic basis of resistance. Here, we report the discovery of Fw1 , a dominant gene conferring resistance to Fusarium wilt in strawberry. The Fw1 locus was uncovered in a genome-wide association study of 565 historically and commercially important strawberry accessions genotyped with 14,408 SNP markers. Fourteen SNPs in linkage disequilibrium with Fw1 physically mapped to a 2.3 Mb segment on chromosome 2 in a diploid F. vesca reference genome. Fw1 and 11 tightly linked GWAS-significant SNPs mapped to linkage group 2C in octoploid segregating populations. The most significant SNP explained 85% of the phenotypic variability and predicted resistance in 97% of the accessions tested—broad-sense heritability was 0.96. Several disease resistance and defense-related gene homologs, including a small cluster of genes encoding nucleotide-binding leucine-rich-repeat proteins, were identified in the 0.7 Mb genomic segment predicted to harbor Fw1 . DNA variants and candidate genes identified in the present study should facilitate the development of high-throughput genotyping assays for accurately predicting Fusarium wilt phenotypes and applying marker-assisted selection.

Description: While quantitative PCR (qPCR) is widely recognized as being among the most accurate methods for quantifying gene expression, it is highly dependent on the use of reliable, stably expressed reference genes. With the increased availability of high-throughput methods for measuring gene expression, whole-transcriptome approaches may be increasingly utilized for reference gene selection and validation. In this study, RNA-seq was used to identify a set of novel qPCR reference genes and evaluate a panel of traditional "housekeeping" reference genes in two species of the evolutionary model plant genus Mimulus . More broadly, the methods proposed in this study can be used to harness the power of transcriptomes to identify appropriate reference genes for qPCR in any study organism, including emerging and nonmodel systems. We find that RNA-seq accurately estimates gene expression means in comparison to qPCR, and that expression means are robust to moderate environmental and genetic variation. However, measures of expression variability were only in agreement with qPCR for samples obtained from a shared environment. This result, along with transcriptome-wide comparisons, suggests that environmental changes have greater impacts on expression variability than on expression means. We discuss how this issue can be addressed through experimental design, and suggest that the ever-expanding pool of published transcriptomes represents a rich and low-cost resource for developing better reference genes for qPCR.