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.

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

This review bridges functional and evolutionary aspects of plastid chromosome architecture in land plants and their putative ancestors. We provide an overview on the structure and composition of the plastid genome of land plants as well as the functions of its genes in an explicit phylogenetic and evolutionary context. We will discuss the architecture of land plant plastid chromosomes, including gene content and synteny across land plants. Moreover, we will explore the functions and roles of plastid encoded genes in metabolism and their evolutionary importance regarding gene retention and conservation. We suggest that the slow mode at which the plastome typically evolves is likely to be influenced by a combination of different molecular mechanisms. These include the organization of plastid genes in operons, the usually uniparental mode of plastid inheritance, the activity of highly effective repair mechanisms as well as the rarity of plastid fusion. Nevertheless, structurally rearranged plastomes can be found in several unrelated lineages (e.g. ferns, Pinaceae, multiple angiosperm families). Rearrangements and gene losses seem to correlate with an unusual mode of plastid transmission, abundance of repeats, or a heterotrophic lifestyle (parasites or myco-heterotrophs). While only a few functional gene gains and more frequent gene losses have been inferred for land plants, the plastid Ndh complex is one example of multiple independent gene losses and will be discussed in detail. Patterns of ndh-gene loss and functional analyses indicate that these losses are usually found in plant groups with a certain degree of heterotrophy, might rendering plastid encoded Ndh1 subunits dispensable.

/pdf/the-evolution-of-the-plastid-chromosome-in-land-plants-gene-4mwl68mgqz.pdf

The evolution of the plastid chromosome in land plants: gene content, gene order, gene function.

The pophelper r package and web app are software tools to aid in population structure analyses. They can be used for the analyses and visualization of output generated from population assignment programs such as admixture, structure and tess. Some of the functions include parsing output run files to tabulate data, estimating K using the Evanno method, generating files for clumpp and functionality to create barplots. These functions can be streamlined into standard r analysis workflows. The latest version of the package is available on github (https://github.com/royfrancis/pophelper). An interactive web version of the pophelper package is available which covers the same functionalities as the r package version with features such as interactive plots, cluster alignment during plotting, sorting individuals and ordering of population groups. The interactive version is available at http://pophelper.com/.

pophelper: an R package and web app to analyse and visualize population structure.

The genus Citrus, comprising some of the most widely cultivated fruit crops worldwide, includes an uncertain number of species Here we describe ten natural citrus species, using genomic, phylogenetic and biogeographic analyses of 60 accessions representing diverse citrus germ plasms, and propose that citrus diversified during the late Miocene epoch through a rapid southeast Asian radiation that correlates with a marked weakening of the monsoons A second radiation enabled by migration across the Wallace line gave rise to the Australian limes in the early Pliocene epoch Further identification and analyses of hybrids and admixed genomes provides insights into the genealogy of major commercial cultivars of citrus Among mandarins and sweet orange, we find an extensive network of relatedness that illuminates the domestication of these groups Widespread pummelo admixture among these mandarins and its correlation with fruit size and acidity suggests a plausible role of pummelo introgression in the selection of palatable mandarins This work provides a new evolutionary framework for the genus Citrus The origin, evolution and domestication of Citrus and the genealogy of the most important wild and cultivated citrus varieties Citrus fruits are one of the most cultivated crops worldwide, yet the evolutionary relationships among citrus species remain uncertain Daniel Rokhsar, Manuel Talon and colleagues analyse the genomes of 60 accessions that represent a diverse range of citrus species, including 30 newly sequenced citrus genomes They characterize the diversity and evolution of citrus at the species level and identify interspecific citrus hybrids and admixtures—genetic mixing between previously isolated populations—that could be the result of human activities such as migration and agriculture The authors identify 10 progenitor species and suggest that citrus originated in southeast Asia, diversifying during the late Miocene epoch through a rapid southeast Asian radiation that correlated with a changing climate, including the weakening of the monsoons They also find extensive relatedness among mandarins and sweet oranges, showing a complex history of admixture during the domestication of these groups

/pdf/genomics-of-the-origin-and-evolution-of-citrus-5fgzjcg5az.pdf

Genomics of the origin and evolution of Citrus

Transposable elements (TEs) are the key players in generating genomic novelty by a combination of the chromosome rearrangements they cause and the genes that come under their regulatory sway. Genome size, gene content, gene order, centromere function, and numerous other aspects of nuclear biology are driven by TE activity. Although the origins and attitudes of TEs have the hallmarks of selfish DNA, there are numerous cases where TE components have been co-opted by the host to create new genes or modify gene regulation. In particular, epigenetic regulation has been transformed from a process to silence invading TEs and viruses into a key strategy for regulating plant genes. Most, perhaps all, of this epigenetic regulation is derived from TE insertions near genes or TE-encoded factors that act in trans. Enormous pools of genome data and new technologies for reverse genetics will lead to a powerful new era of TE analysis in plants.

The Contributions of Transposable Elements to the Structure, Function, and Evolution of Plant Genomes

Summary
Olive (Olea europaea ssp. europaea) is the most important oil fruit crop in temperate areas, but the origin of the cultivated olive remains unclear. The existence of one or several domestication events in the Mediterranean Basin (MB) is still debated.
We analyzed a dataset of 387 cultivated and wild accessions that were genotyped at 25 simple-sequence repeat (SSR) loci. The sample represented genetic diversity at the geographic extremes of the MB. We inferred relationships among samples and also applied approximate Bayesian computation to estimate the most probable demographic model of our samples.
Cultivated olives clustered into three different gene pools (Q1, Q2 and Q3), corresponding loosely to the west, central and eastern MB, respectively. Q1 consisted primarily of accessions from southern Spain, retained the fingerprint of a genetic bottleneck, and was closely related to accessions from the eastern MB. Q2 showed signs of recent admixture with wild olives and may derive from a local domestication event in the central MB.
Overall our results suggest that admixture shaped olive germplasm and perhaps also local domestication events.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.13181

Olive domestication and diversification in the Mediterranean Basin

Olive is one of the most ancient crop plants and the World Olive Germplasm Bank of Cordoba (WOGBC), Spain, is one of the world’s largest collections of olive germplasm. We used 33 SSR (Simple Sequence Repeats) markers and 11 morphological characteristics of the endocarp to characterise, identify and authenticate 824 trees, representing 499 accessions from 21 countries of origin, from the WOGBC collection. The SSR markers exhibited high variability and information content. Of 332 cultivars identified in this study based on unique combinations of SSR genotypes and endocarp morphologies, 200 were authenticated by genotypic and morphological markers matches with authentic control samples. We found 130 SSR genotypes that we considered as molecular variants because they showed minimal molecular differences but the same morphological profile than 48 catalogued cultivars. We reported 15 previously described and 37 new cases of synonyms as well as 26 previously described and seven new cases of homonyms. We detected several errors in accession labelling, which may have occurred at any step during establishment of plants in the collection. Nested sets of 5, 10 and 17 SSRs were proposed to progressively and efficiently identify all of the genotypes studied here. The study provides a useful protocol for the characterisation, identification and authentication of any olive germplasm bank that has facilitated the establishment of a repository of true-to-type cultivars at the WOGBC.

Identification of the Worldwide Olive Germplasm Bank of Córdoba (Spain) using SSR and morphological markers

Genomics and the Contrasting Dynamics of Annual and Perennial Domestication.

It is still an open question as to whether genome size (GS) variation is shaped by natural selection. One approach to address this question is a population-level survey that assesses both the variation in GS and the relationship of GS to ecological variants. We assessed GS in Zea mays, a species that includes the cultivated crop, maize, and its closest wild relatives, the teosintes. We measured GS in five plants of each of 22 maize landraces and 21 teosinte populations from Mexico sampled from parallel altitudinal gradients. GS was significantly smaller in landraces than in teosintes, but the largest component of GS variation was among landraces and among populations. In maize, GS correlated negatively with altitude; more generally, the best GS predictors were linked to geography. By contrast, GS variation in teosintes was best explained by temperature and precipitation. Overall, our results further document the size flexibility of the Zea genome, but also point to a drastic shift in patterns of GS variation since domestication. We argue that such patterns may reflect the indirect action of selection on GS, through a multiplicity of phenotypes and life-history traits.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.12247

Concepción M. Díez

Papers

Olive domestication and diversification in the Mediterranean Basin

Identification of the Worldwide Olive Germplasm Bank of Córdoba (Spain) using SSR and morphological markers

Genomics and the Contrasting Dynamics of Annual and Perennial Domestication.

Genome size variation in wild and cultivated maize along altitudinal gradients.

Epigenetics and plant genome evolution.