Tatiana Arias

Bio: Tatiana Arias is an academic researcher from Tecnológico de Antioquia. The author has contributed to research in topics: Phylogenetic tree & Genome. The author has an hindex of 7, co-authored 23 publications receiving 339 citations. Previous affiliations of Tatiana Arias include University of Washington & University of Hong Kong.

Diversification times among Brassica (Brassicaceae) crops suggest hybrid formation after 20 million years of divergence

Abstract:  Premise of the study: Cruciferous vegetables, many of which are in the genus Brassica (Brassicaceae), are prized for their nutritive value and have been cultivated for thousands of years There are numerous wild northwestern Mediterranean species in the tribe Brassiceae, and it is therefore assumed this center of diversity is also the region of origin Within the tribe, the Nigra and Oleracea clades contain the three diploid Brassica crops, B oleracea , B rapa , and B nigra These three species hybridized in the past to form the tetraploid crop species B juncea , B carinata , and B napus Collectively, these crop Brassicas have been thought to be closely related because they can still hybridize  Methods: Using a combination of molecular phylogenetics, diversifi cation analysis, and historical biogeography, we evaluated the relationships and origins of four nested clades: the tribe Brassiceae, the Nigra-Oleracea clade, the core Oleracea (includes B oleracea + B rapa and their respective wild relatives), and Brassica oleracea and relatives  Key results: We found evidence that the tribe originated around the intersection forming between the Arabian Peninsula and Saharan Africa approximately 24 million years ago (Mya) Our data also suggest that the maternal genomes of the three diploid crop Brassicas are not closely related and that the Nigra-Oleracea clade diverged 20 Mya Finally, our analyses indicate that the core Oleracea lineage giving rise to B oleracea + B rapa originated ≈ 3 Mya in the northeastern Mediterranean, from where ancestors of B oleracea spread through Europe and B rapa to Asia  Conclusions: These results challenge previous hypotheses about the biogeographic origins of the tribe Brassiceae and the crop Brassica species and appear to be correlated with major geological and climatic events in the Mediterranean basin

A fully resolved chloroplast phylogeny of the brassica crops and wild relatives (Brassicaceae: Brassiceae): Novel clades and potential taxonomic implications

Abstract: Brassicas boast an enormous diversity of economically important products. Strikingly, relationships among main lineages are still unknown. The phylogeny of the tribe Brassiceae (Brassicaceae) was reconstructed for 89 species using four plastid regions (rpl32-trnL, atpI-atpH, psbD-trnT, ycf6-psbM ). Representatives of almost all genera were sampled, covering the entire natural range of the tribe from Central Asia to the western Mediterranean, including four previously unsampled genera (Ammosperma, Eremophyton, Fezia, Pseudofortuynia). Phylogenetic analysis recovered eight well-supported clades in the tribe including a new African clade (Henophyton) comprised of genera that have not been previously sampled. Relationships within and between the eight major clades are strongly supported for the first time. The earliest-divergent lineages in the tribe are the clades Vella and Zilla. Henophyton is sister to the clade that includes the lineages Nigra, Crambe, Cakile, Savignya, and Oleracea. Core Brassiceae—a new clade defined here—is comprised of two subclades: (1) Nigra, Crambe, and Cakile and (2) Savignya and Oleracea. Within the Oleracea lineage, a new Core Oleracea clade is defined. Several genera were confirmed to be polyphyletic or paraphyletic, including Brassica, Erucastrum, Sinapis, Diplotaxis and Cakile. Economically important spe- cies belonging to the genera Brassica were primarily distributed across the two most species-rich lineages, Nigra or Oleracea. Collectively, the finding of these novel clades has numerous taxonomic implications.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

Abstract: EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

The Atlantic salmon genome provides insights into rediploidization

Abstract: The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.

Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times

Abstract: The estimation of phylogenetic divergence times from sequence data is an important component of many molecular evolutionary studies. There is now a general appreciation that the procedure of divergence dating is considerably more complex than that initially described in the 1960s by Zuckerkandl and Pauling (1962, 1965). In particular, there has been much critical attention toward the assumption of a global molecular clock, resulting in the development of increasingly sophisticated techniques for inferring divergence times from sequence data. In response to the documentation of widespread departures from clocklike behavior, a variety of local- and relaxed-clock methods have been proposed and implemented. Local-clock methods permit different molecular clocks in different parts of the phylogenetic tree, thereby retaining the advantages of the classical molecular clock while casting off the restrictive assumption of a single, global rate of substitution (Rambaut and Bromham 1998; Yoder and Yang 2000).

The pangenome of an agronomically important crop plant Brassica oleracea

Abstract: There is an increasing awareness that as a result of structural variation, a reference sequence representing a genome of a single individual is unable to capture all of the gene repertoire found in the species. A large number of genes affected by presence/absence and copy number variation suggest that it may contribute to phenotypic and agronomic trait diversity. Here we show by analysis of the Brassica oleracea pangenome that nearly 20% of genes are affected by presence/absence variation. Several genes displaying presence/absence variation are annotated with functions related to major agronomic traits, including disease resistance, flowering time, glucosinolate metabolism and vitamin biosynthesis.