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)

Genetics and analysis of quantitative traits

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.

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

Tomato and salinity

Species are the unit of analysis in many global change and conservation biology studies; however, species are not uniform entities but are composed of different, sometimes locally adapted, populations differing in plasticity We examined how intraspecific variation in thermal niches and phenotypic plasticity will affect species distributions in a warming climate We first developed a conceptual model linking plasticity and niche breadth, providing five alternative intraspecific scenarios that are consistent with existing literature Secondly, we used ecological niche-modeling techniques to quantify the impact of each intraspecific scenario on the distribution of a virtual species across a geographically realistic setting Finally, we performed an analogous modeling exercise using real data on the climatic niches of different tree provenances We show that when population differentiation is accounted for and dispersal is restricted, forecasts of species range shifts under climate change are even more pessimistic than those using the conventional assumption of homogeneously high plasticity across a species' range Suitable population-level data are not available for most species so identifying general patterns of population differentiation could fill this gap However, the literature review revealed contrasting patterns among species, urging greater levels of integration among empirical, modeling and theoretical research on intraspecific phenotypic variation

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The effects of phenotypic plasticity and local adaptation on forecasts of species range shifts under climate change

The Mediterranean olive tree (Olea europaea subsp. europaea) was one of the first trees to be domesticated and is currently of major agricultural importance in the Mediterranean region as the source of olive oil. The molecular bases underlying the phenotypic differences among domesticated cultivars, or between domesticated olive trees and their wild relatives, remain poorly understood. Both wild and cultivated olive trees have 46 chromosomes (2n). A total of 543 Gb of raw DNA sequence from whole genome shotgun sequencing, and a fosmid library containing 155,000 clones from a 1,000+ year-old olive tree (cv. Farga) were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries. Assembly gave a final genome with a scaffold N50 of 443 kb, and a total length of 1.31 Gb, which represents 95 % of the estimated genome length (1.38 Gb). In addition, the associated fungus Aureobasidium pullulans was partially sequenced. Genome annotation, assisted by RNA sequencing from leaf, root, and fruit tissues at various stages, resulted in 56,349 unique protein coding genes, suggesting recent genomic expansion. Genome completeness, as estimated using the CEGMA pipeline, reached 98.79 %. The assembled draft genome of O. europaea will provide a valuable resource for the study of the evolution and domestication processes of this important tree, and allow determination of the genetic bases of key phenotypic traits. Moreover, it will enhance breeding programs and the formation of new varieties.

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Genome sequence of the olive tree, Olea europaea

The possibility of using in vitro shoot apex culture to evaluate salt tolerance of cultivated (Lycopersicon esculentum Mill.) and wild (Lycopersicon pennellii (Correll) D'Arcy) tomato species was determined and related to the response obtained by callus culture. Both apices and calluses were grown on media supplemented with 0, 35, 70, 105, 140, 175 and 210 mM NaCl, and growth and physiological traits were determined. Most apices of L. esculentum did not develop roots from low NaCl levels, whereas the apices of L. pennellii were able to develop roots at the different salt levels. This different degree of salt tolerance between L. esculentum and L. pennellii was not, however, clearly shown on the basis of the shoot growth of the plantlets. The callus response was similar to that shown by the rooting parameters, as callus growth in response to increased salinity was much greater in L. pennellii than in the tomato cultivar. K+decreased more and proline accumulated less with salinity in shoots of L. esculentum compared to L. pennellii, whereas the opposite response was obtained in calluses. The results obtained in this study suggest that rooting parameters are the most useful traits for rapid evaluation and screening of tomato species and segregating populations through in vitro shoot apex culture.

Evaluation of salt tolerance in cultivated and wild tomato species through in vitro shoot apex culture

SummaryTomato seeds (Lycopersicon esculentum Mill.) cvs Pera, Muchamiel, P-73 and GC-72, were primed with 0,0.5 and 1.0 M NaCl solutions. The plants were then grown at 35,70 and 140 mM NaCl. These salt treatments were applied pre-emergence (seed sowing) and post-emergence (4 leaf stage). The effect of seed priming on yield was different depending on both the NaCl concentration used for seed priming and on the time of starting the salt treatments during the growing period of the plants. The yield increase under 1.0 M NaCl priming was mainly due to increased fruit weight, but was always reduced by increasing the NaCl treatment (35-140 mM). The effect of this seed priming on yield was higher when salt treatments were applied pre- rather than post-emergence, although it was significant only in plants treated at 35 and 70 mM NaCl. At pre-emergence, the yield increased in cvs Pera, Muchamiel and GC-72, whereas at post-emergence only cv. GC-72 increased its yield by salt priming. The increase in yield of cv. GC-...

Effect of NaCl priming on increased salt tolerance in tomato

Additional index words. growth stage, Lycopersicon esculentum, NaCl tolerance, shoot Cl, Na and K ion concentrations Abstract. The effects of increasing salinity on dry weight and ion concentration of shoots at various growth stages and on fruit yield in four tomato (Lycopersicon esculentum Mill.) genotypes were assessed. The salt treatments (35, 70, and 140 mM NaCl) were applied pre-emergence (seed sowing) (pre-E) and post-emergence (four-leaf stage) (post-E) and maintained during plant growth. Genotype salt tolerance, measured as shoot dry weight in response to increases in salt concentration, varied depending on plant growth stage and salt application time. When salt was applied pre-E, salt tolerance increased with plant age, whereas when applied post-E, 45-day-old plants were the most salt tolerant. Mature plants were similarly salt tolerant independent of the growth stage at which the salt treatments began. However, fruit yield of all genotypes was higher when salt was applied pre-E than post-E. Shoot dry weight decreased as shoot Cl and Na ion concentrations increased. During early growth stages, pre-E salt-treated plants had the highest Cl-and Na + concentrations and the lowest shoot dry weights. However, at the advanced stages, shoot Cl- and Na + Concentrations were equal for both salt application times. These results show that the plants must adapt to salinity during a period that allows them to develop a mechanism to regulate internal Cl- and Na+ concentrations and, thus, grow under high salinity. Salt tolerance is a complex trait. Breeders developing crops tolerant to saline soils have found few traits that can be used as markers for reliably assessing salt tolerance. In theory, phenotypic markers for salt tolerance should be easy to measure and should be expressed during seed germination, at the seedling stage, or at advanced growth stages. However, the plant's response to salinity can vary with growth stage (Shannon, 1985). Some have argued that, in certain crops, selecting for salt tolerance at the early growth stages may not correlate with the crop's tolerance at later growth stages (Ashraf and McNeilly, 1988; Kingsbury and Epstein, 1984). In many salinity studies, one harvest date has been used to correlate growth with the physiological responses to salinity. The results from such studies can be misleading when genotypes, species, or salinity treatments are compared (Hunt, 1982). Generally, salt tolerance in tomato has been evaluated only at germination (Jones, 1986), during early plant development (Guerrier, 1984), or at maturation (Bolarin et al., 1991). However, some authors have reported that the salt tolerance of young tomato plants did not correlate highly with that of mature plants (Norlyn and Epstein, 1984; Shannon et al., 1987). Furthermore, Caro et al. (1991) pointed out that the ranking of salt-tolerant tomato geno- types based on vegetative characteristics in mature plants may differ from a ranking based on fruit yield. We report the effects of increasing salinity at pre-emergence (pre-E) and post-emergence (post-E) on growth and ion concentra- tions of tomato plants at several growth stages and on fruit yield and its relationship to shoot dry weight, with the objective of defining patterns of variation in the response to salinity shown by 30, 45, 100, and 180-day-old plants.

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Growth, Fruit Yield, and Ion Concentration in Tomato Genotypes after Pre- and Post-emergence Salt Treatments

If in vitro culture is to be used for evaluating the salt tolerance of tomato hybrids and segregant populations in a breeding programme, it is previously necessary to get quick and reliable traits. In this work, growth and physiological responses to salinity of two interspecific hybrids between the cultivated tomato (Lycopersicon esculentum Mill) and its wild salt-tolerant species L pennellii are compared to those of their parents. The leaf callus of the first subculture was grown on media amended with 0, 35, 70, 105, 140, 175 and 210 mM NaCl for 40 days. Relative fresh weight growth of callus in response to increased salinity in the culture medium was much greater in L pennellii than in the tomato cultivars, and greater in the hybrids than in the wild species. Moreover, the different salt tolerance degree of hybrids was related to that of female parents. At high salt levels, only Cl(-) accumulation was higher in L pennellii than in tomato cultivars, whereas in the hybrids both Cl(-), and Na(+) accumulation were higher than in their parents. Proline increased with salinity in the callus of all genotypes; these increases were much higher in the tomato cultivars than in L pennellii, and the hybrids showed a similar response to that of the wild species. Salt-treated callus of the tomato cultivars showed significant increases in valine, isoleucine and leucine contents compared to control callus tissue. In contrast, these amino acids in callus tissues of the wild species and hybrids showed a tendency to decrease with increasing salinity.

Emilio Cano

Papers

Genome sequence of the olive tree, Olea europaea

Evaluation of salt tolerance in cultivated and wild tomato species through in vitro shoot apex culture

Effect of NaCl priming on increased salt tolerance in tomato

Growth, Fruit Yield, and Ion Concentration in Tomato Genotypes after Pre- and Post-emergence Salt Treatments

Responses to NaCl stress of cultivated and wild tomato species and their hybrids in callus cultures.