18 Works

Data from: Adaptive responses along a depth and a latitudinal gradient in the endemic seagrass Posidonia oceanica

Marlene Jahnke, Daniela D’ Esposito, Luigi Orrù, Antonella Lamontanara, Emanuela Dattolo, Fabio Badalamenti, Silvia Mazzuca, Gabriele Procaccini & Luisa Orsini
Seagrass meadows provide important ecosystem services and are critical to the survival of the associated invertebrate community. However, they are threatened worldwide by human-driven environmental change. Understanding the potential for adaptation of these plants is critical to assess not only their ability to persist under future global change scenarios, but also to assess the persistence of the associated communities. Here, we screened wild population of Posidonia oceanica, an endemic long lived marine plant in the...

Data from: The oceanic biological pump: rapid carbon transfer to depth at continental margins during winter

Laurenz Thomsen, Jacopo Aguzzi, Corrado Costa, Fabio De Leo, Andrea Ogston & Autun Purser
The oceanic biological pump is responsible for the important transfer of CO2-C as POC “Particulate Organic Carbon” to the deep sea. It plays a decisive role in the Earth’s carbon cycle and significant effort is spent to quantify its strength. In this study we used synchronized daily time-series data of surface chlorophyll-a concentrations from the NASA’s MODIS satellite in combination with hourly to daily observations from sea surface buoys and from an Internet Operated Vehicle...

Data from: Neonicotinoid pesticides and nutritional stress synergistically reduce survival in honey bees

Simone Tosi, James C. Nieh, Fabio Sgolastra, Riccardo Cabbri & Piotr Medrzycki
The honey bee (Apis mellifera L.) is a major pollinator whose health is of global concern. Declines in honey bee health are related to multiple factors, including resource quality and pesticide contamination. Intensive agricultural areas with crop monocultures potentially reduce the quality and quantity of available nutrients and expose bee foragers to pesticides. However, there is, to date, no evidence for synergistic effects between pesticides and nutritional stress in animals. The neonicotinoids clothianidin (CLO) and...

Data from: Thermal resilience may shape population abundance of two sympatric congeneric Cotesia species (Hymenoptera: Braconidae)

Reyard Mutamiswa, Honest Machekano, Frank Chidawanyika & Casper Nyamukondiwa
Basal and plasticity of thermal tolerance determine abundance, biogeographical patterns and activity of insects over spatial and temporal scales. For coexisting stemborer parasitoids, offering synergistic impact to the efficacy of biological control, mismatches in thermal tolerance may influence their ultimate impact in biocontrol programs under climate variability. Using laboratory-reared congeneric parasitoid species Cotesia sesamiae and Cotesia flavipes Cameron (Hymenoptera: Braconidae), we examined basal thermal tolerance to understand potential impact of climate variability on their survival...

Nalanthamala psidii supplementary data

, Anita Severn-Ellis, Maritha Schoeman, Philipp Bayer, James K. Hane, Jasper G. Rees, Dave Edwards & Jacqueline Batley

Data from: Evolutionary metabolomics reveals domestication-associated changes in tetraploid wheat kernels

Romina Beleggia, Domenico Rau, Giovanni Laidò, Cristiano Platani, Franca Nigro, Mariagiovanna Fragasso, Pasquale De Vita, Federico Scossa, Alisdair R. Fernie, Zoran Nikoloski & Roberto Papa
Domestication and breeding have influenced the genetic structure of plant populations due to selection for adaptation from natural habitats to agro-ecosystems. Here, we investigate the effects of selection on the contents of 51 primary kernel metabolites and their relationships in three Triticum turgidum L. subspecies (i.e., wild emmer, emmer, durum wheat) that represent the major steps of tetraploid wheat domestication. We present a methodological pipeline to identify the signature of selection for molecular phenotypic traits...

Data from: Combined exposure to sublethal concentrations of an insecticide and a fungicide affect feeding, ovary development and longevity in a solitary bee

Fabio Sgolastra, Xavier Arnan, Riccardo Cabbri, Gloria Isani, Piotr Medrzycki, Dariusz Teper & Jordi Bosch
Pollinators in agroecosystems are often exposed to pesticide mixtures. Even at low concentrations, the effects of these mixtures on bee populations are difficult to predict due to potential synergistic interactions. We orally exposed newly-emerged females of the solitary bee Osmia bicornis to environmentally-realistic levels of clothianidin (neonicotinoid insecticide) and propiconazole (fungicide), singly and in combination. The amount of feeding solution consumed was highest in bees exposed to the neonicotinoid, and lowest in bees exposed to...

Data from: Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing

Nathalie Smitz, Pim Van Hooft, Rasmus Heller, Daniel Cornélis, Philippe Chardonnet, Robert Kraus, Ben J. Greyling, Richard Crooijmans, Martien Groenen, Johan Michaux & Ben Greyling
This study aimed to develop a set of SNP markers with high resolution and accuracy within the African buffalo. Such a set can be used, among others, to depict subtle population genetic structure for a better understanding of buffalo population dynamics. In total, 18.5 million DNA sequences of 76 bp were generated by next generation sequencing on an Illumina Genome Analyzer II from a reduced representation library using DNA from a panel of 13 African...

Data from: Genome-wide mapping of targets of maize histone deacetylase hda101 reveals its function and regulatory mechanism during seed development

Hua Yang, Xinye Liu, Mingming Xin, Jinkun Du, Zhaorong Hu, Huiru Peng, Vincenzo Rossi, Qixin Sun, Zhongfu Ni & Yingyin Yao
Histone deacetylases (HDACs) control histone acetylation levels by removing acetyl group from lysine residues. Maize (Zea mays) HDAC HDA101 influences several aspects of development, including kernel size; however, the molecular mechanism by which HDA101 affects kernel development remains unknown. In this study, we find HDA101 regulates the expression of transfer cell-specific genes, suggesting their mis-regulation may be associated with defects in differentiation of transfer cells and smaller kernels of hda101 mutants. To investigate HDA101 function...

Data from: Genetic responsiveness of African buffalo to environmental stressors: a role for epigenetics in balancing autosomal and sex chromosome interactions?

Pim Van Hooft, Eric R. Dougherty, Wayne M. Getz, Barend J. Greyling, Bas J. Zwaan, Armanda D.S. Bastos & Armanda D. S. Bastos
In the African buffalo (Syncerus caffer) population of the Kruger National Park (South Africa) a primary sex-ratio distorter and a primary sex-ratio suppressor have been shown to occur on the Y chromosome. A subsequent autosomal microsatellite study indicated that two types of deleterious alleles with a negative effect on male body condition, but a positive effect on relative fitness when averaged across sexes and generations, occur genome-wide and at high frequencies in the same population....

Data from: Positive selection of deleterious alleles through interaction with a sex-ratio suppressor gene in African buffalo: a plausible new mechanism for a high frequency anomaly

Pim Van Hooft, Ben J. Greyling, Wayne M. Getz, Paul D. Van Helden, Bas J. Zwaan & Armanda D. S. Bastos
Although generally rare, deleterious alleles can become common through genetic drift, hitchhiking or reductions in selective constraints. Here we present a possible new mechanism that explains the attainment of high frequencies of deleterious alleles in the African buffalo (Syncerus caffer) population of Kruger National Park, through positive selection of these alleles that is ultimately driven by a sex-ratio suppressor. We have previously shown that one in four Kruger buffalo has a Y-chromosome profile that, despite...

Data from: Signatures of selection and environmental adaptation across the goat genome post-domestication

Licia Colli, Marco Milanesi, Andrea Talenti, Francesca Bertolini, Minhui Chen, Alessandra Crisà, Kevin Daly, Marcello Del Corvo, Bernt Guldbrandtsen, Johannes A. Lenstra, Ben D. Rosen, Elia Vajana, Gennaro Catillo, Stéphane Joost, Ezequiel Luis Nicolazzi, Estelle Rochat, Max F. Rothschild, Bertrand Servin, Tad S. Sonstegard, Roberto Steri, Curtis P. Van Tassel, Paolo Ajmone-Marsan, Paola Crepaldi, Alessandra Stella & AdaptMap Consortium
Background: Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of goat breeds and these are classified mainly into two types: (i) adaptation to different breeding systems and/or purposes and (ii) adaptation to different environments. As a result, approximately 600 goat breeds have developed worldwide; they differ considerably from one another in terms of phenotypic characteristics and are adapted to a wide range of climatic conditions. In this work, we...

Data from: A genome-wide analysis of MADS-box genes in peach [Prunus persica (L.) Batsch]

Christina E. Wells, Elisa Vendramin, Sergio Jimenez Tarodo, Ignazio Verde & Douglas G. Bielenberg
BACKGROUND: MADS-box genes encode a family of eukaryotic transcription factors distinguished by the presence of a highly-conserved ~58 amino acid DNA-binding and dimerization domain (the MADS-box). The central role played by MADS-box genes in peach endodormancy regulation led us to examine this large gene family in more detail. We identified the locations and sequences of 79 MADS-box genes in peach, separated them into established subfamilies, and broadly surveyed their tissue-specific and dormancy-induced expression patterns using...

Data from: Colonization of the Mediterranean Basin by the vector biting midge species Culicoides imicola: an old story

Stephanie Jacquet, Claire Garros, Eric Lombaert, Catherine Walton, Johana Restrepo, Xavier Allene, Thierry Baldet, Catherine Cetre-Sossah, Alexandra Chaskopoulou, Jean-Claude Delecolle, Amelie Desvars, Mouloud Djerbal, Moussa Fall, Laetitia Gardes, Michel De Garine-Wichatitsky, Maria Goffredo, Yuval Gottlieb, Assane Gueye Fall, Muo Kasina, Karien Labuschagne, Youssef Lhor, Javier Lucientes, Thibaud Martin, Bruno Mathieu, Miguel Miranda … & J.-C. Delecolle
Understanding the demographic history and genetic make-up of colonizing species is critical for inferring population sources and colonization routes. This is of main interest for designing accurate control measures in areas newly colonized by vector species of economically important pathogens. The biting midge Culicoides imicola is a major vector of orbiviruses to livestock. Historically, the distribution of this species was limited to the Afrotropical region. Entomological surveys first revealed the presence of C. imicola in...

Data from: New insights on water buffalo genomic diversity and post-domestication migration routes from medium density SNP chip data

Licia Colli, Marco Milanesi, Elia Vajana, Daniela Iamartino, Lorenzo Bomba, Francesco Puglisi, Marcello Del Corvo, Ezequiel Luis Nicolazzi, Sahar Saad El-Din Ahmed, Jesus Rommel V. Herrera, Libertado Cruz, Shuju Zhang, Aixin Liang, Gouhua Hua, Ligou Yang, Xingjie Hao, Fuyuan Zuo, Song-Jia Lai, Shuilian Wang, Ruyu Liu, Yundeng Gong, Mahdi Mokhber, Yongjiang Mao, Feng Guan, Augustin Vlaic … & Liguo Yang
The domestic water buffalo is native to the Asian continent but through historical migrations and recent importations, nowadays has a worldwide distribution. The two types of water buffalo, i.e., river and swamp, display distinct morphological and behavioral traits, different karyotypes and also have different purposes and geographical distributions. River buffaloes from Pakistan, Iran, Turkey, Egypt, Romania, Bulgaria, Italy, Mozambique, Brazil and Colombia, and swamp buffaloes from China, Thailand, Philippines, Indonesia and Brazil were genotyped with...

Data from: SNP genotyping elucidates the genetic diversity of Magna Graecia grapevine germplasm and its historical origin and dissemination

Gabriella De Lorenzis, Francesco Mercati, Carlo Bergamini, Maria Francesca Cardone, Antonio Lupini, Antonio Mauceri, Angelo Raffale Caputo, Loredana Abbate, Maria Gabriella Barbagallo, Donato Antonacci, Francesco Sunseri & Lucio Brancadoro
Background: Magna Graecia is the ancient name used to label the area of South of Italy extensively populated by Greek colonizers. Archeological and historical evidences identified in this region the oldest winegrowing area in Italy, pointing out its importance in the spread of high specialized viticulture around the Mediterranean Sea shores. In this work, the genetic diversity of Magna Graecia grape germplasm was assessed and its role in the grapevine propagation around the Mediterranean basin...

Data from: Retrotransposon proliferation coincident with the evolution of dioecy in asparagus

Alex Harkess, Francesco Mercati, Loredana Abbate, Michael McKain, J. Chris Pires, Tea Sala, Francesco Sunseri, Agostino Falavigna & Jim Leebens-Mack
Current phylogenetic sampling reveals that dioecy and an XY sex chromosome pair evolved once or possibly twice in the genus Asparagus. Although there appear to be some lineage-specific polyploidization events, the base chromosome number of 2n=2x=20 is relatively conserved across the Asparagus genus. Regardless, dioecious species tend to have larger genomes than hermaphroditic species. Here we test whether this genome size expansion in dioecious species is related to a polyploidization and subsequent chromosome fusion or...

Chromosome evolution and the genetic basis of agronomically important traits in greater yam

Jessen Bredeson, Jessica Lyons, Ibukun Oniyinde, Nneka Okereke, Olufisayo Kolade, Ikenna Nnabue, Nneka Okereke, Christian Nwadili, Eva Hribova, Matthew Parker, Jeremiah Nwogha, Shengqiang Shu, Joseph Carlson, Robert Kariba, Samuel Muthemba, Katarzyna Knop, Geoffrey Barton, Anna Sherwood, Antonio Lopez-Montes, Robert Asiedu, Ramni Jamnadass, Alice Muchugi, David Goodstein, Chiedozie Egesi, Jonathan Featherston … & Daniel Rokhsar
The nutrient-rich tubers of the greater yam, Dioscorea alata L., provide food and income security for millions of people around the world. Despite its global importance, however, greater yam remains an ‘orphan crop.’ Here we address this resource gap by presenting a highly contiguous chromosome-scale genome assembly of D. alata combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient allotetraploidization in the Dioscorea lineage, followed by extensive...

Registration Year

  • 2021
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  • 2018
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    3
  • 2016
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  • 2015
    2
  • 2014
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Resource Types

  • Dataset
    18

Affiliations

  • Agricultural Research Council
    18
  • University of California, Berkeley
    3
  • Wageningen University & Research
    3
  • University of KwaZulu-Natal
    3
  • University of Pretoria
    2
  • University of Bologna
    2
  • Donald Danforth Plant Science Center
    1
  • Institute for Coastal Marine Environment
    1
  • University of Adelaide
    1
  • Sao Paulo State University
    1