15 Works

Data from: Transcriptional variation associated with cactus host plant adaptation in Drosophila mettleri

Kim Hoang, Luciano M. Matzkin & Jeremy M. Bono
Although the importance of host plant chemistry in plant–insect interactions is widely accepted, the genetic basis of adaptation to host plants is not well understood. Here, we investigate transcriptional changes associated with a host plant shift in Drosophila mettleri. While D. mettleri is distributed mainly throughout the Sonoran Desert where it specializes on columnar cacti (Carnegiea gigantea and Pachycereus pringleii), a population on Santa Catalina Island has shifted to chemically divergent coastal prickly pear cactus...

Data from: Diversity and population structure of northern switchgrass as revealed through exome capture sequencing

Joseph Evans, Emily Crisovan, Kerrie Barry, Chris Daum, Jerry Jenkins, Govindarajan Kunde-Ramamoorthy, Aruna Nandety, Chew Yee Ngan, Brieanne Vaillancourt, Chia-Lin Wei, Jeremy Schmutz, Shawn M. Kaeppler, Michael D. Casler, Carol Robin Buell & Chia-Lin Wei
Switchgrass (Panicum virgatum L.) is a polyploid, perennial grass species that is native to North America, and is being developed as a future biofuels feedstock crop. Switchgrass is present primarily in two ecotypes: a northern upland ecotype composed of tetraploid and octoploid accessions, and a southern lowland ecotype composed of primarily tetraploid accessions. We employed high-coverage exome capture sequencing (~2.4 Tb) to genotype 537 individuals from 45 upland and 21 lowland populations. From these data,...

The tepary bean genome provides insight into evolution and domestication under heat stress

Samira Mafi Moghaddam, Atena Oladzad, Chu Shin Koh, Larissa Ramsay, John Hart, Sujan Mamidi, Genevieve Hoopes, Avinash Sreedasyam, Andrew Wiersma, Dongyan Zhao, Jane Grimwood, John P. Hamilton, Jerry Jenkins, Brieanne Vaillancourt, Joshua C. Wood, Jeremy Schmutz, Sateesh Kahale, Tiomothy Porch, Kirstin E. Bett, C. Robin Buell & Phillip E. McClean
Tepary bean (Phaseolus acutifolis A. Gray), native to the Sonoran Desert, is highly adapted to heat and drought. It is a sister species of common bean (Phaseolus vulgaris L.), the most important legume protein source for direct human consumption, and whose production is threatened by climate change. Analysis of the tepary genome revealed mechanisms for resilience to moderate heat stress and a reduced disease resistance gene repertoire, consistent with adaptation to arid, hot environments. Extensive...

Data from: Phylogeography and adaptation genetics of stickleback from the Haida Gwaii archipelago revealed using genome-wide SNP genotyping

Bruce E. Deagle, Felicity C. Jones, Devin M. Absher, David M. Kingsley & Thomas E. Reimchen
Threespine stickleback populations are model systems for studying adaptive evolution and the underlying genetics. In lakes on the Haida Gwaii archipelago (off western Canada), stickleback have undergone a remarkable local radiation and show phenotypic diversity matching that seen throughout the species distribution. To provide a historical context for this radiation, we surveyed genetic variation at >1000 single nucleotide polymorphism (SNP) loci in stickleback from over 100 populations. SNPs included markers evenly distributed throughout genome and...

Data from: Enhanced stability and polyadenylation of select mRNAs support rapid thermogenesis in the brown fat of a hibernator

Katharine R. Grabek, Cecilia Diniz Behn, Gregory S. Barsh, Jay R. Hesselberth & Sandra L. Martin
During hibernation, animals cycle between torpor and arousal. These cycles involve dramatic but poorly understood mechanisms of dynamic physiological regulation at the level of gene expression. Each cycle, Brown Adipose Tissue (BAT) drives periodic arousal from torpor by generating essential heat. We applied digital transcriptome analysis to precisely timed samples to identify molecular pathways that underlie the intense activity cycles of hibernator BAT. A cohort of transcripts increased during torpor, paradoxical because transcription effectively ceases...

Switchgrass v5 4-way (AP13 x DAC, WBC x VS16) genetic map

John Lovell, Adam Healey, Jeremy Schmutz & Thomas Juenger
Here we present the genetic map construction methods for the switchgrass 4-way mapping population. The map spans 750 recombinant 4-way (pseudo F2) progeny genotyped at 4700 markers. These data are formatted for simple input into R/qtl and most other QTL mapping programs.

Data from: Recurrent evolution of melanism in South American felids

Alexsandra Schneider, Corneliu Henegar, Kenneth Day, Devin Absher, Constanza Napolitano, Leandro Silveira, Victor A. David, Stephen J. O’Brien, Marilyn Menotti-Raymond, Gregory S. Barsh & Eduardo Eizirik
Morphological variation in natural populations is a genomic test bed for studying the interface between molecular evolution and population genetics, but some of the most interesting questions involve non-model organisms that lack well annotated reference genomes. Many felid species exhibit polymorphism for melanism but the relative roles played by genetic drift, natural selection, and interspecies hybridization remain uncertain. We identify mutations of Agouti signaling protein (ASIP) or the Melanocortin 1 receptor (MC1R) as independent causes...

Data from: Extensive genetic diversity is present within North American switchgrass germplasm

Joseph Evans, Millicent D. Sanciangco, Kin H. Lau, Emily Crisovan, Kerrie Barry, Chris Daum, Hope Hundley, Jerry Jenkins, Megan Kennedy, Govindarajan Kunde-Ramamoorthy, Brieanne Vaillancourt, Ananta Acharya, Jeremy Schmutz, Malay Saha, Shawn M. Kaeppler, E. Charles Brummer, Michael D. Casler & C. Robin Buell
Switchgrass (Panicum virgatum L.) is a perennial native North American grass present in two ecotypes: upland, found primarily in the northern range of switchgrass habitats, and lowland, found largely in the southern reaches of switchgrass habitats. Previous studies focused on a diversity panel of primarily northern switchgrass, so to expand our knowledge of genetic diversity in a broader set of North American switchgrass, exome capture sequence data were generated for 632 additional, primarily lowland individuals....

Genotyping-by-sequencing data for a Haitian sorghum breeding program

Geoffrey Morris, Terry Felderhoff, Noah Winans, Rachel Walstead, Jean Rigaud Charles, Gael Pressoir & Kebede Muleta
Rapid environmental change can lead to extinction of populations or evolutionary rescue via genetic adaptation. In the past several years, smallholder and commercial cultivation of sorghum (Sorghum bicolor), a global cereal and forage crop, has been threatened by a global outbreak of an aggressive new biotype of sugarcane aphid (SCA; Melanaphis sacchari). Here we characterized genomic signatures of adaptation in a Haitian sorghum breeding population, which had been recently founded from admixed global germplasm, extensively...

QTL × environment interactions underlie adaptive divergence in switchgrass across a large latitudinal gradient

David Lowry, John Lovell, Li Zhang, Jason Bonnette, Philip Fay, Robert Mitchell, John Lloyd-Reilley, Arvid Boe, Yanqi Wu, Francis Rouquette, Richard Wynia, Xiaoyu Weng, Kathrine Behrman, Adam Healey, Kerrie Barry, Anna Lipzen, Diane Bauer, Aditi Sharma, Jerry Jenkins, Jeremy Schmutz, Felix B. Fritschi & Thomas E. Juenger
Local adaptation is the process by which natural selection drives adaptive phenotypic divergence across environmental gradients. Theory suggests that local adaptation results from genetic trade-offs at individual genetic loci, where adaptation to one set of environmental conditions results in a cost to fitness in alternative environments. However, the degree to which there are costs associated with local adaptation is poorly understood because most of these experiments rely on two-site reciprocal transplant experiments. Here, we quantify...

Data from: Developmental mechanisms of stripe patterns in rodents

Ricardo Mallarino, Corneliu Henegar, Mercedes Mirasierra, Marie Manceau, Carsten Schradin, Mario Vallejo, Slobodan Beronja, Gregory S. Barsh & Hopi E. Hoekstra
Mammalian colour patterns are among the most recognizable characteristics found in nature and can have a profound impact on fitness. However, little is known about the mechanisms underlying the formation and subsequent evolution of these patterns. Here we show that, in the African striped mouse (Rhabdomys pumilio), periodic dorsal stripes result from underlying differences in melanocyte maturation, which give rise to spatial variation in hair colour. We identify the transcription factor ALX3 as a regulator...

Genomic variation within the maize Stiff Stalk heterotic germplasm pool

Nolan Bornowski, Kathryn J. Michel, John P. Hamilton, Shujun Ou, Arun S. Seetharam, Jerry Jenkins, Jane Grimwood, Chris Plott, Shengqiang Shu, Jayson Talag, Megan Kennedy, Hope Hundley, Vasanth R. Singan, Kerrie Barry, Chris Daum, Yuko Yoshinaga, Jeremy Schmutz, Candice N. Hirsch, Matthew B. Hufford, Natalia De Leon, Shawn M. Kaeppler & C. Robin Buell
The Stiff Stalk heterotic group is an important source of inbreds used in U.S. commercial hybrid production. Founder inbreds B14, B37, B73, and to a lesser extent B84, are found in the pedigrees of a majority of commercial seed parent inbred lines. We created high-quality genome assemblies of B84 and four ex-Plant Variety Protection lines LH145 representing B14, NKH8431 of mixed descent, PHB47 representing B37, and PHJ40 which is a Pioneer Hi-Bred early Stiff Stalk...

Data from: The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes

Dimitrios Floudas, Manfred Binder, Robert Riley, Kerrie Barry, Robert A. Blanchette, Bernard Henrissat, Angel T. Martínez, Robert Ortillar, Joseph W. Spatafora, Jagjit S. Yadav, Andrea Aerts, Isabelle Benoit, Alex Boyd, Alexis Carlson, Alex Copeland, Pedro M. Coutinho, Ronald P. De Vries, Patricia Ferreira, Keisha Findley, Brian Foster, Jill Gaskell, Dylan Glotzer, Paweł Górecki, Joseph Heitman, Cedar Hesse … & David S. Hibbett
Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non–lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as...

Data from: Generation of transcript assemblies and identification of single nucleotide polymorphisms from seven lowland and upland cultivars of switchgrass

Kevin L. Childs, Aruna Nandety, Candice N. Hirsch, Elsa Góngora-Castillo, Jeremy Schmutz, Shawn M. Kaeppler, Michael D. Casler & C. Robin Buell
Switchgrass (Panicum virgatum) is a North American perennial prairie species that has been used as a rangeland and forage crop and has recently been targeted as a potential biofuel feedstock species. Switchgrass, which occurs as tetraploid and octoploid forms, is classified into lowland or upland ecotypes that differ in growth phenotypes and adaptation to distinct habitats. Using RNA-sequencing reads derived from crown, young shoot and leaf tissues, we generated sequence data from seven switchgrass cultivars,...

Supporting data for: Gene-rich UV sex chromosomes harbor conserved regulators of sexual development (Carey et al., 2021)

Sarah Carey, Shenqiang Shu, John Lovell, Avinash Shenqiang, Florian Maumus, George Tiley, Noe Fernandez-Pozo, Kerrie Barry, Cindy Chen, Mei Wang, Anna Lipzen, Chris Daum, Christopher Saski, Adam Payton, Jordan McBreen, Roth Conrad, Leslie Kollar, Sanna Olsson, Sanna Huttunen, Jacob Landis, Norman Wickett, Matthew Johnson, Stefan Rensing, Jane Grimwood, Jeremy Schmutz … & Adam Healey
Non-recombining sex chromosomes, like the mammalian Y, often lose genes and accumulate transposable elements, a process termed degeneration. The correlation between suppressed recombination and degeneration is clear in animal XY systems, but the absence of recombination is confounded with other asymmetries between the X and Y. In contrast, UV sex chromosomes, like those found in bryophytes, experience symmetrical population genetic conditions. Here we generate and use nearly gapless female and male chromosome-scale reference genomes of...

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  • HudsonAlpha Institute for Biotechnology
  • Michigan State University
  • Joint Genome Institute
  • University of Wisconsin-Madison
  • Great Lakes Bioenergy Research Center
  • The University of Texas at Austin
  • University of Minnesota
  • Howard Hughes Medical Institute
  • Fred Hutchinson Cancer Research Center
  • Stanford University