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Data from: Genome scans reveal candidate domestication and improvement genes in cultivated sunflower, as well as post-domestication introgression with wild relatives.
Baute, Gregory J.; Kane, Nolan C.; Grassa, Christopher J.; Lai, Zhao; Rieseberg, Loren H. — 2015-12-02 • The development of modern crops typically involves both selection and hybridization, but to date most studies have focused on the former. In the present study we explore how both processes, and their interactions, have molded the genome of the cultivated sunflower, a globally important oilseed. • To identify genes targeted by selection during the domestication and improvement of sunflower, and to detect post-domestication hybridization with wild species, we analyzed transcriptome sequences of 80 genotypes, including wild, landrace, and modern lines of Helianthus annuus, as well as two cross-compatible wild relatives, H. argophyllus and H. petiolaris. • Outlier analyses identified 122 and 15 candidate genes associated with domestication and improvement, respectively. As in several previous studies, genes putatively involved in oil biosynthesis were the most extreme outliers. Additionally, several promising associations were observed with previously mapped QTLs, such as branching. Admixture analyses revealed that all of the modern cultivar genomes we examined contained one or more introgressions from wild populations, with every chromosome having evidence of introgression in at least one modern line. • Cumulatively, introgressions cover approximately 10% of the cultivated sunflower genome. Surprisingly, introgressions do not avoid candidate domestication genes likely because of the re-introduction of branching.
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Data from: Recent non-hybrid origin of sunflower ecotypes in a novel habitat
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Rieseberg, Loren H.; Andrew, Rose L.; Kane, Nolan C.; Baute, Greg J.; Grassa, Christopher J. — 2012-09-17 The genomics of local adaptation is an increasingly active field, providing insights into the forces driving ecological speciation and the repeatability of evolution. Demography and gene flow play an important role in determining the paths by which parallel evolution occurs and the genomic signatures of adaptation. In the annual sunflowers, hybridization between species has repeatedly led to the colonization of extreme habitats, such as sand dunes. In a new case of adaptation to sand dunes that occurs in populations of H. petiolaris growing at Great Sand Dunes National Park and Preserve (Colorado), we wished to determine the age and long-term migration patterns of the system, as well as its ancestry. We addressed these questions with restriction-associated DNA (RAD) sequence data, aligned to a reference transcriptome. In an isolation with migration model using RAD sequences, coalescent analysis showed that the dune ecotype originated since the last ice age, which is very recent compared with the hybrid dune species, H. anomalus. Large effective population sizes and substantial numbers of gene migrants per generation between dune and nondune ecotypes explained the highly heterogeneous divergence observed among loci. Analysis of RAD-derived SNPs identified heterogeneous divergence between the dune and nondune ecotypes, as well as identifying its nearest relative. Our results did not support the hypothesis that the dune ecotype has hybrid ancestry, suggesting that adaptation of sunflowers to dunes has occurred by multiple mechanisms. The ancestry and long-term history of gene flow between incipient sunflower species provides valuable context for our understanding of ecological speciation and parallel adaptation.
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Data from: Mandated data archiving greatly improves access to research data
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Vines, Timothy H.; Andrew, Rose L.; Bock, Dan G.; Franklin, Michelle T.; Gilbert, Kimberly J.; Kane, Nolan C.; Moore, Jean-Sébastien; Moyers, Brook T.; Renaut, Sébastien; Rennison, Diana J.; Veen, Thor; Yeaman, Sam — 2013-01-04 The data underlying scientific papers should be accessible to researchers both now and in the future, but how best can we ensure that these data are available? Here we examine the effectiveness of four approaches to data archiving: no stated archiving policy, recommending (but not requiring) archiving, and two versions of mandating data deposition at acceptance. We control for differences between data types by trying to obtain data from papers that use a single, widespread population genetic analysis, STRUCTURE. At one extreme, we found that mandated data archiving policies that require the inclusion of a data availability statement in the manuscript improve the odds of finding the data online almost 1000-fold compared to having no policy. However, archiving rates at journals with less stringent policies were only very slightly higher than those with no policy at all. We also assessed the effectiveness of asking for data directly from authors and obtained over half of the requested datasets, albeit with ∼8 d delay and some disagreement with authors. Given the long-term benefits of data accessibility to the academic community, we believe that journal-based mandatory data archiving policies and mandatory data availability statements should be more widely adopted.
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Data from: Genomics of Compositae crops: reference transcriptome assemblies, and evidence of hybridization with wild relatives
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Hodgins, Kathryn A.; Lai, Zhao; Oliveira, Luiz O.; Still, David W.; Scascitelli, Moira; Barker, Michael S.; Kane, Nolan C.; Dempewolf, Hannes; Kozik, Alex; Kesseli, Richard V.; Burke, John M.; Michelmore, Richard W.; Rieseberg, Loren H. — 2013-08-19 Although the Compositae harbours only two major food crops, sunflower and lettuce, many other species in this family are utilized by humans and have experienced various levels of domestication. Here we have used next generation sequencing technology to develop 15 reference transcriptome assemblies for Compositae crops or their wild relatives. These data allow us to gain insight into the evolutionary and genomic consequences of plant domestication. Specifically, we performed Illumina sequencing of Cichorium endivia, Cichorium intybus, Echinacea angustifolia, Iva annua, Helianthus tuberosus, Dahlia hybrida, Leontodon taraxacoides and Glebionis segetum, as well 454 sequencing of Guizotia scabra, Stevia rebaudiana, Parthenium argentatum and Smallanthus sonchifolius. Illumina reads were assembled using Trinity, and 454 reads were assembled using MIRA and CAP3. We evaluated the coverage of the transcriptomes using BLASTX analysis of a set of ultra-conserved orthologs (UCOs) and recovered most of these genes (88-98%). We found a correlation between contig length and read length for the 454 assemblies, and greater contig lengths for the 454 compared to the Illumina assemblies. This suggests that longer reads can aid in the assembly of more complete transcripts. Finally, we compared the divergence of orthologs at synonymous sites (Ks) between Compositae crops and their wild relatives and found greater divergence when the progenitors were self-incompatible. We also found greater divergence between pairs of taxa that had some evidence of post-zygotic isolation. For several more distantly related congeners, such as chicory and endive, we identified a signature of introgression in the distribution of Ks values.

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(auteur : Kane, Nolan C.)

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