Adriana Alberti
A5068749773- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Protist diversity and phylogeny
- Wheat and Barley Genetics and Pathology
- Plant Disease Resistance and Genetics
- Chromosomal and Genetic Variations
- Environmental DNA in Biodiversity Studies
- Bacteriophages and microbial interactions
- Genetic diversity and population structure
- Coral and Marine Ecosystems Studies
- Genetic and phenotypic traits in livestock
- Genetic Mapping and Diversity in Plants and Animals
- Plant Virus Research Studies
- Marine and coastal ecosystems
- Banana Cultivation and Research
- Carcinogens and Genotoxicity Assessment
- Plant Diversity and Evolution
- Marine and environmental studies
- Fungal and yeast genetics research
- Microbial Metabolic Engineering and Bioproduction
- Genomics and Chromatin Dynamics
- Photosynthetic Processes and Mechanisms
- Genetics, Aging, and Longevity in Model Organisms
- Plant tissue culture and regeneration
- Plant Taxonomy and Phylogenetics
Centre National de la Recherche Scientifique
2012-2025
Université Paris-Saclay
2019-2025
Commissariat à l'Énergie Atomique et aux Énergies Alternatives
2015-2024
Genoscope
2015-2024
Institut de Biologie Intégrative de la Cellule
2021-2024
CEA Paris-Saclay
2019-2024
Azienda Socio Sanitaria Territoriale degli Spedali Civili di Brescia
2023-2024
Azienda Sanitaria Unità Locale di Reggio Emilia
2024
University of Brescia
2002-2022
Institute for Microelectronics and Microsystems
2014-2022
Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture functional diversity, microbial community structure, and their ecological determinants remains grand challenge. We analyzed 7.2 terabases metagenomic data from 243 Tara Oceans samples 68 locations in epipelagic mesopelagic waters across the globe to generate an ocean reference gene catalog with >40 million nonredundant, mostly novel sequences viruses, prokaryotes, picoeukaryotes. Using 139...
Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and oleracea, followed chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms high gene content. We examined consequences its recent duplication. The constituent An Cn subgenomes are engaged in subtle structural, functional, epigenetic cross-talk, abundant homeologous...
An ordered draft sequence of the 17-gigabase hexaploid bread wheat (Triticum aestivum) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across homeologous chromosomes and subgenomes. Comparative analysis subgenomes extant diploid tetraploid relatives showed that high similarity structural conservation are retained, with limited loss, after polyploidization. However, genomes there was evidence dynamic gain,...
Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to well-studied Poales, which include cereals. vital for food security in many tropical subtropical countries most popular fruit industrialized countries. The Musa domestication process started some 7,000 years ago Southeast Asia. It involved hybridizations between diverse species subspecies, fostered by human migrations, selection diploid triploid...
Vertebrate evolution has been shaped by several rounds of whole-genome duplications (WGDs) that are often suggested to be associated with adaptive radiations and evolutionary innovations. Due an additional round WGD, the rainbow trout genome offers a unique opportunity investigate early fate duplicated vertebrate genome. Here we show after 100 million years two ancestral subgenomes have remained extremely collinear, despite loss half protein-coding genes, mostly through pseudogenization. In...
Viruses influence ecosystems by modulating microbial population size, diversity, metabolic outputs, and gene flow. Here, we use quantitative double-stranded DNA (dsDNA) viral-fraction metagenomes (viromes) whole viral community morphological data sets from 43 Tara Oceans expedition samples to assess patterns structure in the upper ocean. Protein cluster cataloging defined pelagic upper-ocean pan core suggested that this sequence space is well-sampled. Analyses of protein clusters,...
The allohexaploid bread wheat genome consists of three closely related subgenomes (A, B, and D), but a clear understanding their phylogenetic history has been lacking. We used assemblies five diploid relatives to analyze genome-wide samples gene trees, as well estimate evolutionary relatedness divergence times. show that the A B genomes diverged from common ancestor ~7 million years ago these gave rise D through homoploid hybrid speciation 1 2 later. Our findings imply present-day is product...
Coffee, tea, and chocolate converge Caffeine has evolved multiple times among plant species, but no one knows whether these events involved similar genes. Denoeud et al. sequenced the Coffea canephora (coffee) genome identified a conserved gene order (see Perspective by Zamir). Although this species underwent fewer duplications than related relevant caffeine genes experienced tandem that expanded their numbers within species. Scientists have seen independent expansions in distantly of tea...
We produced a reference sequence of the 1-gigabase chromosome 3B hexaploid bread wheat. By sequencing 8452 bacterial artificial chromosomes in pools, we assembled 774 megabases carrying 5326 protein-coding genes, 1938 pseudogenes, and 85% transposable elements. The distribution structural functional features along revealed partitioning correlated with meiotic recombination. Comparative analyses indicated high wheat-specific inter- intrachromosomal gene duplication activities that are...
Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic genomic compositions, little is known about how transcriptomes vary globally. Here, we present a dataset 187 metatranscriptomes 370 metagenomes from 126 globally distributed sampling stations establish resource 47 million genes to study community-level across depth layers pole-to-pole. We examine gene expression changes community...
While our knowledge about the roles of microbes and viruses in ocean has increased tremendously due to recent advances genomics metagenomics, research on marine microbial eukaryotes zooplankton benefited much less from these new technologies because their larger genomes, enormous diversity, largely unexplored physiologies. Here, we use a metatranscriptomics approach capture expressed genes open Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster...
Allohexaploid bread wheat ( Triticum aestivum L.) provides approximately 20% of calories consumed by humans. Lack genome sequence for the three homeologous and highly similar genomes (A, B, D) has impeded expression analysis grain transcriptome. We used previously unknown information to analyze cell type–specific genes in developing identified distinct co-expression clusters reflecting spatiotemporal progression during endosperm development. observed no global but type– stage-dependent...
Emergence of polyphagous herbivorous insects entails significant adaptation to recognize, detoxify and digest a variety host-plants. Despite its biological practical importance - since eat 20% crops no exhaustive analysis gene repertoires required for adaptations in generalist insect herbivores has previously been performed. The noctuid moth Spodoptera frugiperda ranks as one the world's worst agricultural pests. This is while majority other lepidopteran are specialist. It consists two...
The evolutionary basis of domestication has been a longstanding question and its genetic architecture is becoming more tractable as domestic species become genome-enabled. Before established worldwide, sheep goats were domesticated in the fertile crescent 10,500 years before present (YBP) where their wild relatives remain. Here we sequence genomes Asiatic mouflon Bezoar ibex goat center compare with that domestics from local, traditional, improved breeds. Among genomic regions carrying...
Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem players, RNA insufficiently studied outside disease settings. In this study, we analyzed ≈28 terabases of Global Ocean sequences expand Earth's virus catalogs their taxonomy, investigate evolutionary origins, assess marine biogeography from pole pole. Using new approaches optimize discovery classification, identified that necessitate substantive revisions taxonomy (doubling phyla adding >50% classes)...
Long-read sequencing technologies were launched a few years ago, and in contrast with short-read technologies, they offered promise of solving assembly problems for large complex genomes. Moreover by providing long-range information, it could also solve haplotype phasing. However, existing long-read still have several limitations that complicate their use most research laboratories, as well and/or genome projects. In 2014, Oxford Nanopore released the MinION® device, small low-cost...
Abstract A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009–2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks recent advances in field genomics, extensive sequencing has been performed for a deep genomic analysis this huge samples. strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics metatranscriptomics, chosen size-fractionated...
Abstract During the last glacial–interglacial cycle, Arctic biotas experienced substantial climatic changes, yet nature, extent and rate of their responses are not fully understood 1–8 . Here we report a large-scale environmental DNA metagenomic study ancient plant mammal communities, analysing 535 permafrost lake sediment samples from across spanning past 50,000 years. Furthermore, present 1,541 contemporary genome assemblies that were generated as reference sequences. Our provides several...
DNA viruses are increasingly recognized as influencing marine microbes and microbe-mediated biogeochemical cycling. However, little is known about global RNA virus diversity, ecology, ecosystem roles. In this study, we uncover patterns predictors of community- “species”-level diversity contextualize their ecological impacts from pole to pole. Our analyses revealed four zones, latitudinal depth patterns, environmental correlates for viruses. findings only partially parallel those cosampled...
Recent advances in genomics indicate functional significance of a majority genome sequences and their long range interactions. As detailed examination organization function requires very high quality sequence, the objective this study was to improve reference assembly banana (Musa acuminata). We have developed modular bioinformatics pipeline sequence assemblies, which can handle various types data. The comprises several semi-automated tools. However, unlike classical automated tools that are...
The duplication of mammalian genomes is under the control a spatiotemporal program that orchestrates positioning and timing firing replication origins. molecular mechanisms coordinating activation about predicted origins remain poorly understood, partly due to intrinsic rarity bubbles, making it difficult purify short nascent strands (SNS). precise identification based on high-throughput sequencing SNS constitutes new methodological challenge. We propose statistical method with controlled...