Benchmark of algorithms for multiple DNA sequence alignment across livestock species

Background: Due to the growing amount of biological data, it is often necessary to select the most optimal estimation method for DNA sequence alignment across livestock species. One of the most important benches of genomics is to modelling homology between considered DNA sequences. A multiple sequence alignment is a potent tool for molecular and evolutionary biology, and there are several programs and algorithms applicable for this purpose. The purpose of this paper was to study the most commonly used DNA alignment algorithms to select the optimal tool dedicated for short sequences.Methods: Four steps of bioinformatics pipelines were considered to benchmark the algorithms for multiple DNA sequence alignment across livestock species: 1) selection of reference genome sequences of ARS1.2 for cattle, EquCab3.0 for horse and vicPac2 for alpaca with a low E-value using TBLASTn 2) removing gaps for these sequences 3) alignment of obtained sequences using examined algorithms 4) matching the quality of aligned sequences with sequences of reference genomes by more software. The time of computation was archived for the whole analysis. The seven programs were utilized, each based on different alignment algorithms, namely: ClustalO, ClustalW, Kalign, MAFFT, MUSCLE, Probcons and T-Coffee.Results: The result obtained in this study showed that the fastest is progressive algorithms such as Kalign or MUSCLE-FAST. Moreover, the iterative algorithms like MAFFT and MUSCLE revealed a higher quality of the alignment. The T-Coffee and Probcons programs were computational cost-effective; simultaneously, they were generating a medium-quality calculation in a relatively long time. The best quality of alignment was shown by iterative variants of the MAFFT program; however, the speed of the calculations was relatively low. The fastest algorithm was Kalign, making alignment much faster than the competitors, but achieving average results in the quality of the alignment. The average speed ratio concerning the quality of the analyzed algorithms was obtained by the progressive version of MAFFT, NS1.Conclusions: We conclude that the results of this study can be used to re-alignment of variant primers in new livestock genome releases

Reduced pollen viability and achene development in Solidago ×niederederi Khek from Poland

Pollen and achene characters of natural interspecific hybrid Solidago ×niederederi Khek were analyzed and compared with putative parental species S. virgaurea L. and S. canadensis L. to estimate the level of disturbances in generative reproduction resulting from its hybrid nature. Pollen viability (stainability) of Solidago ×niederederi from one newly discovered locality in NE Poland was evidently reduced to ~65% in both viability tests (acetocarmine and Alexander). The diameter of viable pollen (median 21.11 µm) fell between S. canadensis (median 19.52 µm) and S. virgaurea (median 23.48 µm). Both parental species produced normally developed achenes with high frequency (~90%) whereas in the hybrid, the seed set was dramatically low (6%). The results clearly indicated that sexual reproduction of hybridogenous taxon S. ×niederederi is disturbed, and its potential impact as an invasive species depends mainly on vegetative propagation

Usefulness of morphological characters in determination of intra- and interspecific diversity of violets (Viola L., Violaceae)

The genus ViolaL. with more than 500 species is difficult taxonomic group due to great intraspecific morphological variability resulted from the influence of environmental conditions but also from hybridization. Interspecific hybrids form hybrid swarm or introgressants, therefore species discrimination still remains a problem in this genus. To analyze intra- and interspecific variability the species from two sections were studied. Intraspecific (intra- and interpopulation) differentiation were analyzed in V. tricolorL. (section Melanium) from non-polluted and polluted with heavy metals sites. Intra- and interspecific variability with the influence of hybridization were studied in V. reichenbachiana Jord. ex Boreau – V. riviniana Rchb. group (section Viola). V. tricoloris a species very differentiated morphologically (intra- and interpopulation variability). It occupies metalliferous (Zn, Pb, Cd, Cu) and non-metalliferous sites in its geographic range. We analyzed morphological and anatomical features in metallicolous and non-metallicolous populations to determine the differences influenced by environmental conditions. In field observations, plants within both population types were quite variable, but interpopulation differences in some characters were evident (plant height, stem branching, number of flowers per plant, hairiness of whole plant and leaf, leaf shape and color, petal color, plant height, spur length, seed length). Correspondence analysis (CA) based on a data matrix of 12 selected qualitative and quantitative characters indicated that in terms of morphological variation the metallicolous populations did not possess common characters separating them from the non-metallicolous populations (Słomka et al. 2012). V. reichenbachianaand V. rivinianaare closely related species and due to a lack of prezygotic isolation mechanisms they hybridize in nature and easily produce interspecific hybrids and introgressive forms which occur sympatrically. Multivariate statistical analyses (MSA) based on 50 morphological characters of vegetative and generative organs showed significant differences between V. reichenbachianaand V. riviniana from non-polluted by heavy metals areas, high level of its intra- and interpopulational variability and the occurrence of interspecific hybrids. Plants from metal-polluted sites were very viable and formed a cluster of intermediate morphotypes between V. reichenbachianaand V. riviniana with some individuals included into V. riviniana range (Migdałek et al.2013, in press)

Evaluation of analytical protocols of alignment mapping tools using high throughput next-generation genome sequencing data

Background: Ever since the development of first next-generation genome sequencer (NGS) in 2005, there are rapid developments of high throughput next-generation genome sequencing (HT-NGS) techniques and tools used in genetics and genomics has become much more comfortable and cheaper. The result is the generation of a massive amount of data sets, requiring detailed analysis, which becomes impossible without the use of appropriate bioinformatics tools. One of the crucial steps in the analysis of NGS data is to map readings to a reference sequence. Although the dominance of Illumina synthesis by sequencing (SBS) technology has been noticeable in recent years, the choice of the tools is hampered and the variety of input data and reference genomes. Moreover, the tools used are crucial for result files and further analysis.Methods: The subject of this paper is the three most frequently used alignment mapping programs, which have functions to allow working with many platforms: BWA, Bowtie2 and SMALT. The task of the tested aligners is to match short sequences coming from NGS with reference sequences. The most popular: BWA and Bowtie2 use for this purpose the Burrows-Wheeler transformation and SMALT maps the sequences using hashing and dynamic programming. The presented paper aimed to compare the quality and efficiency of the alignment mapping programs under examination, due to three criteria: i) the quality of the compared sequences of different lengths and from different platforms; ii) coefficient of wrongly compared sequences; iii) the computational resources used.Results: By comparing the results of the mapping analyses for all the programs used, the least popular SMALT is the best. Obtaining the highest percentage of mapped readings for each platform and maintaining the lowest computational memory usage, turns out to be the most optimal choice.Conclusions: The results presented in this paper can be used to verify and rebuild data analysis pipelines from NGS based so far on other tools. We conclude that by using the tools under appropriate conditions, it is possible to improve the quality of the analyses, speed them up and reduce their cost

Genotype-dependent mass somatic embryogenesis: a chance to recover extinct populations of Pulsatilla vulgaris Mill.

The paper presents a technique for micropropagation of endangered in Europe and extinct in Poland Pulsatilla vulgaris for ex situ conservation of the genetic resources. Genotype-dependent induction of somatic embryogenesis and rooting was revealed in series of two experiments (I and II) performed under the same experimental conditions. Shoot tips of seedlings were the best explants in both experiments and Murashige and Skoog (MS) medium supplemented with 0.25 or 0.5 mg L− 1 BAP was suitable for induction of somatic embryos (SE) and adventitious shoots. Mass SE was obtained in experiment I after explants transfer on ½ MS (2% sucrose) + 0.45 mg L− 1 B1 and extending culture to 2–3 months without passages. Rooting of adventitious shoots was a critical point. Out of seven rooting media used in experiment I, only two, ½ MS hormone free (2% sucrose) + 0.45 mg L− 1 B1 or MS + 5 mg L− 1 NAA + 3.76 mg L− 1 B2 resulted in altogether 36.4% rooted shoots. In experiment II, somatic embryogenesis, rooting and acclimatization of adventitious shoots failed. Regenerated plantlets and seedlings converted from SE from experiment I were acclimatized to ex vitro conditions. Both genome size, determined by flow cytometry, and genetic diversity analyzed by ISSR markers, confirmed the compatibility of regenerants from experiment I with P. vulgaris initial seedlings and commercial cultivar. Regenerants obtained in experiment II differed genetically from the regenerants of experiment I and cultivar. Propagated in vitro tissues/organs (SE, adventitious shoots) of P. vulgaris could be a source of material for cryopreservation, artificial seed production and/or for acclimatization of regenerated plantlets and could be used for restoration of the extinct populations. Key Message The micropropagation technique via organogenesis and somatic embryogenesis of endangered in Europe pasqueflower was developed as a tool for species recovery. The critical point is that somatic embryogenesis is genotype-dependent, which affects the repeatability of the experiments and also impose

Binarization of hand roentgenograms

Celem tej pracy było porównanie kilku metod binaryzacji cyfrowych obrazów rentgenowskich dłoni. Zostało użytych sześć metod progowania: Otsu, rekurencyjna metoda Otsu, Entropii, Niblack’a, Sauvoli oraz Bernsena. Aby zilustrować wyniki zastosowania tych algorytmów do rentgenogramów napisana została aplikacja do przetwarzania obrazów.Pierwsze trzy ze wspomnianych wcześniej metod używały jednej, globalnej wartości progu dla całego obrazu i sprawdziły się bardzo dobrze w zadaniu odnajdywania maski, która może być wykorzystana w dalszym przetwarzaniu. Metody Niblacka, Sauvoli i Bernsena obliczają wartość progu dla każdego piksela oddzielnie, przez co są znacznie wolniejsze a ich wyniki bardziej zaszumione, jednakże sprawdzają się do wyszukiwania konturu obrazu. Badania wykazały, iż nie ma jednej uniwersalnej metody binaryzacji a wybór metody powinien zależeć od celu dalszego przetwarzania obrazu.The purpose of this thesis was to compare several methods of digital hand roentgenograms binarization. There were six methods of thresholding used: Otsu, recursive Otsu, Entropy, Niblack, Sauvola and Bernsen. Image processing application was developed to illustrate the results of applying these algorithms to digital roentgenograms.The first three of aforementioned methods were using one global threshold value for the entire image and performed very well on finding a mask that can be used in further image processing. Niblack, Sauvola and Bernsen methods calculate threshold value for every pixel separately thus are much slower and their results are noisier but are well suitable for finding image contours. The studies have shown that there is no universal method of binarization and a method selection should be based on the purpose of further image processing