The coffee genome provides insight into the convergent evolution of caffeine biosynthesis

Denœud, France; Carretero‐Paulet, Lorenzo; Dereeper, Alexis; Droc, Gaëtan; Guyot, Romain; Pietrella, Marco; Zheng, Chunfang; Alberti, Adriana; Anthony, François; Aprea, Giuseppe; Aury, Jean‐Marc; Bento, Pascal; Bernard, Maria; Bocs, Stéphanie; Campa, Claudine; Cenci, Alberto; Combes, Marie‐Christine; Crouzillat, Dominique; Silva, Corinne Da; Daddiego, Loretta; Bellis, Fabien De; Dussert, Stéphane; Garsmeur, Olivier; Gayraud, Thomas; Guignon, Valentin; Jahn, Katharina; Jamilloux, Véronique; Joët, Thierry; Labadie, Karine; Lan, Tianying; Leclercq, Julie; Lepelley, Maud; Leroy, Thierry; Li, Leiting; Librado, Pablo; Lopez, Loredana; Muñoz, Adriana; Noël, Benjamin; Pallavicini, Alberto; Perrotta, Gaetano; Poncet, Valérie; Pot, David; Priyono, Priyono; Rigoreau, Michel; Rouard, Mathieu; Rozas, Julio; Tranchant‐Dubreuil, Christine; VanBuren, Robert; Zhang, Qiong; Andrade, Alan Carvalho; Argout, Xavier; Bertrand, Benoît; Kochko, Alexandre de; Graziosi, G.; Henry, Robert J.; Jayarama,; Ming, Ray; Nagai, Chifumi; Rounsley, Steve; Sankoff, David; Giuliano, Giovanni; Albert, Victor A.; Wincker, Patrick; Lebailly, Philippe

doi:10.1126/science.1255274

Cited by 517 publications

(571 citation statements)

References 161 publications

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“…DNA transposons were annotated with a custom pipeline that includes the 'gt tirvish' command, which is part of the GenomeTools suite 42 . The age of LTR-RTs was determined by obtaining a likelihood divergence estimate between the LTRs with baseml from PAML 43 16 , coffee 17 and lettuce 15 and with grape 18 as the outgroup. Identification of orthology and paralogy relationships, measurements of sequence divergence and estimation of divergence time through the level of synonymous substitutions were performed as detailed in Supplementary Note 3.1 on the basis of the methods described in ref.…”

Section: Letter Research Methodsmentioning

confidence: 99%

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The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

Badouin¹,

Gouzy²,

Grassa³

et al. 2017

Nature

574

645

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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 1 . Even greater resilience is achievable through the mining of resistance alleles from compatible wild sunflower relatives 2,3 , including numerous extremophile species 4 . 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 5 and required single-molecule realtime 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 6 and a sunflowerspecific whole-genome duplication around 29 million years ago 7 . 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 8,9 .As the only major crop domesticated in North America, with its sunlike inflorescence that inspired artists, the sunflower is both a social icon and a major research focus for scientists. In evolutionary biology, the Helianthus genus is a long-time model for hybrid speciation and adaptive introgression 10 . In plant science, the sunflower is a model for understanding solar tracking 11 and inflorescence development 12 .Despite this large interest, assembling its genome has been extremely difficult as it mainly consists of long and highly similar repeats. This complexity has challenged leading-edge assembly protocols for close to a decade 13 .To finally overcome this challenge, we generated a 102× sequencing coverage of the genome of the inbred line XRQ using 407 singlemolecule real-time (SMRT) cells on the PacBio RS II platform. Production of 32 million very long reads allowed us to generate a genome assembly that captures 3 gigabases (Gb) (80% of the estimated genome size) in 13,957 sequence contigs. Four high-density genetic maps were combined with a sequence-based physical map to build the sequences of the 17 pseudo-chromosomes that anchor 97% of the gene content (Fig.

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Section: Letter Research Methodsmentioning

confidence: 99%

“…17) and grape 18 as an outgroup. The grape genome is considered to be the closest modern representative of the ancestral eudicot karyotype (AEK) consisting of 7 (pre-γ ancestor) or 21 (post-γ ancestor) protochromosomes, with γ indicating the ancestral whole-genome triplication of the Eudicots (WGT-γ ) 19 .…”

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confidence: 99%

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

Badouin¹,

Gouzy²,

Grassa³

et al. 2017

Nature

574

645

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“…The two trees tested are detailed below. To identify gene families specifically expanded in the Cephalotus genome, we followed the method implemented in refs 4 and 61 , accepting a weighted Akaike information criterion (wAIC) ratio of 2.7 for the best-fit branch model to the second-best-fit model. We ran BadiRate 60 twice, once for each of the two alternative topologies shown above.…”

Section: Maximum-likelihood Inference Of Orthogroup Gains and Lossesmentioning

confidence: 99%

“…Long-terminal repeat retrotransposons account for 76% of the genome (Supplementary Tables 3 and 4). Syntenic block comparison with the robusta coffee genome, which maintained diploidy since the ancient split from the Cephalotus lineage 4 , reveals mostly one-to-one mappings ( Fig. 1c and Supplementary Table 5), indicating that the Cephalotus genome has not experienced further whole genome duplications since the hexaploidy event at the origin of core eudicots 5 (Supplementary Note 1).…”

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confidence: 99%

Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory

et al. 2017

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Carnivorous plants exploit animals as a nutritional source and have inspired long-standing questions about the origin and evolution of carnivory-related traits. To investigate the molecular bases of carnivory, we sequenced the genome of the heterophyllous pitcher plant Cephalotus follicularis, in which we succeeded in regulating the developmental switch between carnivorous and non-carnivorous leaves. Transcriptome comparison of the two leaf types and gene repertoire analysis identified genetic changes associated with prey attraction, capture, digestion and nutrient absorption. Analysis of digestive fluid proteins from C. follicularis and three other carnivorous plants with independent carnivorous origins revealed repeated co-options of stress-responsive protein lineages coupled with convergent amino acid substitutions to acquire digestive physiology. These results imply constraints on the available routes to evolve plant carnivory.

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“…Examples include the octaploid genome of strawberry. A doubled-haploid line of the highly heterozygous diploid genome of the robusta coffee plant (Coffea canephora; 2n = 2× = 22) has been sequenced 45 . It is one of the parents of the elite coffee plant C. arabica, the tetraploid genome of which has yet to be sequenced.…”

Section: Combined Approaches To Genome Sequencing and Assemblymentioning

confidence: 99%

Genomic innovation for crop improvement

Bevan

Uauy

Wulff

et al. 2017

Nature

312

219

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Crop production needs to increase to secure future food supplies, while reducing its impact on ecosystems. Detailed characterization of plant genome structure and genetic diversity is crucial for meeting these challenges. Advances in genome sequencing and assembly are being used to access to the large and complex genomes of crops and their wild relatives. Sequencing of wild crop relatives is identifying a wide spectrum of genetic variation, permitting the association of genetic diversity with diverse agronomic phenotypes. In combination with improved and automated phenotyping assays and functional genomic studies, genomics is providing new foundations for crop-breeding systems. In the twentieth century, famines caused by political crises, mismanagement of food production or genocide killed an estimated 70 million people and were second only to war as the greatest manmade cause of death 1 . The father of the Green Revolution, Norman Borlaug, summarized the importance of crops: "Without food, people perish, social and political organizations disintegrate, and civilizations collapse. " For thousands of years, people have dedicated considerable resources to securing food supplies; for example, grain supplies to ancient Rome were secured through an extensive network of long-distance transport, and the distribution of grain was coordinated and subsidized by the cura annonae ('care for the grain supply'), an important figure who contributed to the maintenance of political unity and power.During the past 10,000 years, a period known as the Holocene, Earth's environment has been unusually stable. This probably facilitated the domestication of crops from wild species, resulting in steadily improved yields and adaptation to new agricultural areas. The production of food is now carried out on a vast scale, with 38% of Earth's surface dedicated to agriculture 2 . This increased production is having a pervasive influence on ecosystems worldwide: nitrogen production for agriculture accounts for 1.2% of global energy consumption 3 ; photosynthesis can no longer maintain stable levels of atmospheric carbon dioxide; and food production consumes around 70% of freshwater supplies. The modelling of crop responses to increases in temperature predicts that there will be a considerable reduction in the yield of rice, an important crop around the world 4 . Climate change could also alter the dynamics of crop pathogenic agents by altering the range of vectors and by compromising the immune response of crops 5 .Crop production must therefore adapt to more variable environments and the substantial impact it has on the environment needs to be reduced. Productivity must also increase at a much greater rate than in the past to meet the needs of Earth's growing population 6 . Genetic improvements in crop performance continue to be crucial for increasing crop productivity, but current rates of improvement are unable to meet the demands of sustainability and food security 7 . Plant genomics has a central role in the improvement of crops, includi...

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The coffee genome provides insight into the convergent evolution of caffeine biosynthesis

Cited by 517 publications

References 161 publications

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory

Genomic innovation for crop improvement

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