Suchergebnisse

Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness. ; This work was supported by: Argentina: INTA and CONICET. Belgium: Flemish Institute for Biotechnology and Ghent University. China: The State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences; Ministry of Science and Technology (2006AA10A116, 2004CB720405, 2006CB101907, 2007DFB30080) Ministry of Agriculture ('948' Program: 2007-Z5); National Natural Science Foundation (36171319); Postdoctoral Science Foundation (20070420446). EuropeanUnion: FP6 Integrated ProjectEU-SOL PL 016214. France: Institute National de la Recherche Agronomique and Agence/nNationale de la Recherche. Germany: the Max Planck Society. India: Department of Biotechnology, Government of India; Indian Council of Agricultural Research. Italy: Ministry of Research (FIRB-SOL, FIRB-Parallelomics, ItaLyco and GenoPOM projects); Ministry of Agriculture (Agronanotech and Biomassval projects); FILAS foundation; ENEA; CNR-ENEA project L. 191/2009. Japan: Kazusa DNA Research Institute Foundation and National Institute of Vegetable and Tea Science. Korea: KRIBB Basic Research Fund and Crop Functional Genomics Research Center (CFGC), MEST./nNetherlands: Centre for BioSystemsGenomics, Netherlands Organization for Scientific Research. Spain: Fundacio´n Genoma España; Cajamar; FEPEX; Fundación Séneca; ICIA; IFAPA; Fundación Manrique de Lara; Instituto Nacional de Bioinformatica. UK: BBSRC grant BB/C509731/1; DEFRA; SEERAD. USA: NSF (DBI-0116076;/nDBI-0421634; DBI-0606595; IOS-0923312; DBI-0820612; DBI-0605659; DEB-0316614; DBI 0849896 and MCB 1021718); USDA (2007-02773 and 2007-35300-19739); USDA-ARS. We acknowledge the Potato Genome Sequencing Consortiumfor sharing data before publication; potato RNA-Seq data was provided by C. R. Buell from the NSF-funded Potato Genome Sequence and Annotation project; tomato RNA-Seq data by the USDA-funded SolCAP project, N. Sinha and J. Maloof; the Amplicon Express team for BAC pooling services; construction of the Whole Genome Profiling (WGP) physicalmapwas supported by EnzaZaden, RijkZwaan, Vilmorin& Cie,/nand Takii & Co. Keygene N.V. owns patents and patent applications covering its AFLP and Whole Genome Profiling technologies; AFLP and Keygene are registered trademarks of Keygene N.V.

Large-scale gene duplication, including whole-genome duplication (WGD), is a very common phenomenon in eukaryotic genomes. Bursts of gene duplications are considered a major source of evolutionary innovation and have been associated with the increase in biological complexity and adaptive radiations of species (Zhang 2003). In particular, large-scale gene duplications, generally associated with WGDs, have been reported for many eukaryotic lineages including plants (Van de Peer et al. 2017), fungi (Marcet-Houben and Gabaldón 2015), and animals (Taylor et al. 2001). Although large-scale duplication seems less pervasive in animals than in plants, a growing number of studies report such events in animals. Among other lineages, putative WGDs have been described at the base of vertebrates (Ohno 1970; Dehal and Boore 2005; Putnam et al. 2008), and in several lineages of fish (Christoffels et al. 2004; Glasauer and Neuhauss 2014), amphibians (Mable et al. 2011; Session et al. 2016), and arthropods (Jacobson et al. 2013; Kenny et al. 2016; Schwager et al. 2017; Li et al. 2018). Aphids belong to the infraorder Aphidomorpha that includes three families: Aphididae, Adelgidae, and Phylloxeridae (Favret 2013; Nováková et al. 2013; Blackman and Eastop 2000). Aphids and related (Aphidomorpha) species (Becker-Migdisova and Aizenberg 1962) are hemipteran insects that feed on plant sap (Tjallingii 1995). This specialized diet, rich in carbohydrates but poor in nitrogen compounds, has resulted in several adaptations including the establishment of tight relationships with bacterial endosymbionts (Scarborough et al. 2005; Moya et al. 2008; von Dohlen et al. 2017). There are more than 5,000 described aphid species, of which, about 450 have been collected from crop plants, and 100 are considered of significant economic importance (Van Emden and Harrington 2017). Genomes of several aphid species of agricultural interest have been sequenced, including Acyrthosiphon pisum, Myzus persicae, Diuraphis noxia, Aphis glycines, and Sipha flava (International Aphid Genomics Consortium 2010; Nicholson et al. 2015; Mathers et al. 2017; Wenger et al. 2017). However, except for S. flava (subfamily Chaitophorinae), the sequenced aphids belong to a single subfamily, Aphidinae, limiting our understanding of the genomic diversity in this group of insects. Remarkably, most genome analyses in these species have revealed an important number of paralogous sequences and expanded gene families, including amino acid transporters, odorant and gustatory receptor genes, miRNA-specific dicer-1, ago1 genes, and pasha, among others (Smadja et al. 2009; Huerta-Cepas et al. 2010; Jaubert-Possamai et al. 2010; Duncan et al. 2016; Mathers et al. 2017). However, the close relatedness of the sequenced species provides little resolution to the phylogenetic placement of the duplication events, particularly the ancestral ones. Recent studies have focused on assessing patterns of sequence and expression divergence among recently duplicated genes in A. pisum (Fernández et al. 2019) or M. persicae (Mathers et al. 2017). They have also inspected the distribution of old and young A. pisum paralogs along chromosomes, by categorizing the age of genes that are best-reciprocal hits of each other based on the amount of synonymous substitutions (Li et al. 2019). However, we still lack a proper understanding of when the ancestral duplications occurred, and whether they can be linked to phenotypic innovations shared by aphids or related species. To better assess the origin of the paralogous genes of aphids we sequenced the genome of Cinara cedri (Lachninae subfamily, tribe Eulachnini), the first representative genome from an early-branching lineage of the Aphididae family. Cinara species (and most Lachninae) are particular among aphids as they feed on conifers (gymnosperms), whereas all the other genome-sequenced aphids feed on angiosperms. Another clear difference between the Lachninae and the rest of aphids is that two co-obligate endosymbionts (Buchnera aphidicola, Serratia symbiotica) are present in this group, whereas only B. aphidicola is obligate for the rest of aphids (Latorre and Manzano-Marín 2017). We used a phylogeny-based approach (Huerta-Cepas and Gabaldón 2011) to provide the relative timing of aphid duplications in a phylogenetic framework that includes 21 other fully sequenced genomes and two transcriptomes. Our results provide compelling evidence for an ancestral wave of gene duplications, whose origin predates the diversification of all sequenced aphids, adelgids, and phyloxerids, but are subsequent to their divergence from the Coccoidea lineage, ∼106–227 Ma. ; This research was funded by European Regional Development Fund (ERDF) and Ministerio de Economía y Competitividad (Spain) (Grant Nos. PGC2018-099344-B-100 and BFU2015-67107). T.G. group also acknowledges support from the Catalan Research Agency (AGAUR) SGR857, and grants from the European Union's Horizon 2020 research and innovation program under the grant agreements ERC-2016-724173 and MSC-747607. T.G. also receives support from an INB (Grant No. PT17/0009/0023—ISCIII-SGEFI/ERDF). The authors want to thank Sophia Derdak for her help in the genome polishing step. ; Peer Reviewed ; Postprint (published version)

Aphids (Aphidoidea) are a diverse group of hemipteran insects that feed on plant phloem sap. A common finding in studies of aphid genomes is the presence of a large number of duplicated genes. However, when these duplications occurred remains unclear, partly due to the high relatedness of sequenced species. To better understand the origin of aphid duplications we sequenced and assembled the genome of Cinara cedri, an early branching lineage (Lachninae) of the Aphididae family. We performed a phylogenomic comparison of this genome with 20 other sequenced genomes, including the available genomes of five other aphids, along with the transcriptomes of two species belonging to Adelgidae (a closely related clade to the aphids) and Coccoidea. We found that gene duplication has been pervasive throughout the evolution of aphids, including many parallel waves of recent, species-specific duplications. Most notably, we identified a consistent set of very ancestral duplications, originating from a large-scale gene duplication predating the diversification of Aphidomorpha (comprising aphids, phylloxerids, and adelgids). Genes duplicated in this ancestral wave are enriched in functions related to traits shared by Aphidomorpha, such as association with endosymbionts, and adaptation to plant defenses and phloem-sap-based diet. The ancestral nature of this duplication wave (106–227 Ma) and the lack of sufficiently conserved synteny make it difficult to conclude whether it originated from a whole-genome duplication event or, alternatively, from a burst of large-scale segmental duplications. Genome sequencing of other aphid species belonging to different Aphidomorpha and related lineages may clarify these findings. ; This research was funded by European Regional Development Fund (ERDF) and Ministerio de Economía y Competitividad (Spain) (Grant Nos. PGC2018-099344-B-100 and BFU2015-67107). T.G. group also acknowledges support from the Catalan Research Agency (AGAUR) SGR857, and grants from the European Union's Horizon 2020 research and innovation program under the grant agreements ERC-2016-724173 and MSC-747607. T.G. also receives support from an INB (Grant No. PT17/0009/0023—ISCIII-SGEFI/ERDF). ; Peer reviewed

Aphids (Aphidoidea) are a diverse group of hemipteran insects that feed on plant phloem sap. A common finding in studies of aphid genomes is the presence of a large number of duplicated genes. However, when these duplications occurred remains unclear, partly due to the high relatedness of sequenced species. To better understand the origin of aphid duplications we sequenced and assembled the genome of Cinara cedri, an early branching lineage (Lachninae) of the Aphididae family. We performed a phylogenomic comparison of this genome with 20 other sequenced genomes, including the available genomes of five other aphids, along with the transcriptomes of two species belonging to Adelgidae (a closely related clade to the aphids) and Coccoidea. We found that gene duplication has been pervasive throughout the evolution of aphids, including many parallel waves of recent, species-specific duplications. Most notably, we identified a consistent set of very ancestral duplications, originating from a large-scale gene duplication predating the diversification of Aphidomorpha (comprising aphids, phylloxerids, and adelgids). Genes duplicated in this ancestral wave are enriched in functions related to traits shared by Aphidomorpha, such as association with endosymbionts, and adaptation to plant defenses and phloem-sap-based diet. The ancestral nature of this duplication wave (106-227 Ma) and the lack of sufficiently conserved synteny make it difficult to conclude whether it originated from a whole-genome duplication event or, alternatively, from a burst of large-scale segmental duplications. Genome sequencing of other aphid species belonging to different Aphidomorpha and related lineages may clarify these findings. ; This research was funded by European Regional Development Fund (ERDF) and Ministerio de Economía y Competitividad (Spain) (Grant Nos. PGC2018-099344-B-100 and BFU2015-67107). T.G. group also acknowledges support from the Catalan Research Agency (AGAUR) SGR857, and grants from the European Union's Horizon 2020 research and innovation program under the grant agreements ERC-2016-724173 and MSC-747607. T.G. also receives support from an INB (Grant No. PT17/0009/0023—ISCIII-SGEFI/ERDF). The genome, annotation and sequencing reads have been deposited at the European Nucleotide Archive (ENA) under the project accession PRJEB33415