Scaffold filling, contig fusion and comparative gene order inference

<p>Abstract</p> <p>Background</p> <p>There has been a trend in increasing the phylogenetic scope of genome sequencing without finishing the sequence of the genome. Increasing numbers of genomes are being published in scaffold or contig form. Rearrangement algorithms, however, including gene order-based phylogenetic tools, require whole genome data on gene order or syntenic block order. How then can we use rearrangement algorithms to compare genomes available in scaffold form only? Can the comparative evidence predict the location of unsequenced genes?</p> <p>Results</p> <p>Our method involves optimally filling in genes missing from the scaffolds, while incorporating the augmented scaffolds directly into the rearrangement algorithms as if they were chromosomes. This is accomplished by an exact, polynomial-time algorithm. We then correct for the number of extra fusion/fission operations required to make scaffolds comparable to full assemblies. We model the relationship between the ratio of missing genes actually absent from the genome versus merely unsequenced ones, on one hand, and the increase of genomic distance after scaffold filling, on the other. We estimate the parameters of this model through simulations and by comparing the angiosperm genomes <it>Ricinus communis </it>and <it>Vitis vinifera</it>.</p> <p>Conclusions</p> <p>The algorithm solves the comparison of genomes with 18,300 genes, including 4500 missing from one genome, in less than a minute on a MacBook, putting virtually all genomes within range of the method.</p

The genomic Make-Up of a Hybrid Species - Analysis of the Invasive Cottus Lineage (Pisces, Teleostei) in the River Rhine system

In the past years a new invasive lineage of sculpins (Cottus species complex) has been studied that is currently expanding in the Lower River Rhine. Molecular analysis showed that this lineage has originated through hybridization of Cottus perifretum from the River Scheldt and Cottus rhenanus from the Lower River Rhine system. The emergence of the hybrid lineage is correlated with new habitat adaptations that allow the expansion along river habitats that have previously not been used by Cottus. Thus the question arises, if the hybridization event facilitated the invasion of and the adaptation to such a new environment. To start tackling this question an estimate is required how much each of the parental species contributed to the hybrid genome and which chromosomal fragments became fixed. Several genomic resources had to be developed in order to map the ancestries of chromosomal fragments in the hybrid genome. As a basic genomic resource for Cottus a genetic map based on already established microsatellite markers was created. This map was compared with the physical maps of sequenced fish genomes and a high degree of conserved synteny between Cottus and Tetraodon nigroviridis and between Cottus and Gasterosteus aculeatus could be detected. These model fish genomes could then be used as a reference in the further analysis of the Cottus genome. Finally, a set of ancestry-informative markers was developed in order to determine the ancestries of chromosomal fragments in the hybrid lineage. These tools allowed to map the hybrid genome and to assess the contribution of each parental species to the hybrid lineage. 25 genomic fragments could be identified that were fixed for material from only one parental species and thus might harbor genes that are relevant for the specific adaptations in the hybrid species

Twisted Tales: Insights into Genome Diversity of Ciliates Using Single-Cell 'Omics.

The emergence of robust single-cell 'omics techniques enables studies of uncultivable species, allowing for the (re)discovery of diverse genomic features. In this study, we combine single-cell genomics and transcriptomics to explore genome evolution in ciliates (a &gt; 1 Gy old clade). Analysis of the data resulting from these single-cell 'omics approaches show: 1) the description of the ciliates in the class Karyorelictea as "primitive" is inaccurate because their somatic macronuclei contain loci of varying copy number (i.e., they have been processed by genome rearrangements from the zygotic nucleus); 2) gene-sized somatic chromosomes exist in the class Litostomatea, consistent with Balbiani's (1890) observation of giant chromosomes in this lineage; and 3) gene scrambling exists in the underexplored Postciliodesmatophora (the classes Heterotrichea and Karyorelictea, abbreviated here as the Po-clade), one of two major clades of ciliates. Together these data highlight the complex evolutionary patterns underlying germline genome architectures in ciliates and provide a basis for further exploration of principles of genome evolution in diverse microbial lineages

Structural snapshots of Xer recombination reveal activation by synaptic complex remodeling and DNA bending

Bacterial Xer site-specific recombinases play an essential genome maintenance role by unlinking chromosome multimers, but their mechanism of action has remained structurally uncharacterized. Here, we present two high-resolution structures of Helicobacter pylori XerH with its recombination site DNA difH, representing pre-cleavage and post-cleavage synaptic intermediates in the recombination pathway. The structures reveal that activation of DNA strand cleavage and rejoining involves large conformational changes and DNA bending, suggesting how interaction with the cell division protein FtsK may license recombination at the septum. Together with biochemical and in vivo analysis, our structures also reveal how a small sequence asymmetry in difH defines protein conformation in the synaptic complex and orchestrates the order of DNA strand exchanges. Our results provide insights into the catalytic mechanism of Xer recombination and a model for regulation of recombination activity during cell division

The Pathway to Detangle a Scrambled Gene

Programmed DNA elimination and reorganization frequently occur during cellular differentiation. Development of the somatic macronucleus in some ciliates presents an extreme case, involving excision of internal eliminated sequences (IESs) that interrupt coding DNA segments (macronuclear destined sequences, MDSs), as well as removal of transposon-like elements and extensive genome fragmentation, leading to 98% genome reduction in Stylonychia lemnae. Approximately 20-30% of the genes are estimated to be scrambled in the germline micronucleus, with coding segment order permuted and present in either orientation on micronuclear chromosomes. Massive genome rearrangements are therefore critical for development.To understand the process of DNA deletion and reorganization during macronuclear development, we examined the population of DNA molecules during assembly of different scrambled genes in two related organisms in a developmental time-course by PCR. The data suggest that removal of conventional IESs usually occurs first, accompanied by a surprising level of error at this step. The complex events of inversion and translocation seem to occur after repair and excision of all conventional IESs and via multiple pathways.This study reveals a temporal order of DNA rearrangements during the processing of a scrambled gene, with simpler events usually preceding more complex ones. The surprising observation of a hidden layer of errors, absent from the mature macronucleus but present during development, also underscores the need for repair or screening of incorrectly-assembled DNA molecules

Populations of doubled haploids for genetic mapping in hexaploid winter triticale.

To create a framework for genetic dissection of hexaploid triticale, six populations of doubled haploid (DH) lines were developed from pairwise hybrids of high-yielding winter triticale cultivars. The six populations comprise between 97 and 231 genotyped DH lines each, totaling 957 DH lines. A consensus genetic map spans 4593.9&nbsp;cM is composed of 1576 unique DArT markers. The maps reveal several structural rearrangements in triticale genomes. In preliminary tests of the populations and maps, markers specific to wheat segments of the engineered rye chromosome 1R (RM1B) were identified. Example QTL mapping of days to heading in cv. Krakowiak revealed loci on chromosomes 2BL and 2R responsible for extended vernalization requirement, and candidate genes were identified. The material is available to all parties interested in triticale genetics

The Effect of X-Rays on Cytological Traits of Tuta absoluta (Lepidoptera: Gelechiidae)

The tomato leafminer, Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae) is one of the most important pests of tomato. With the purpose of developing environmentally friendly control tactics such as the inherited sterility (IS) technique against this species, it is essential to understand its genetics and biology. In this paper we analyzed the karyotype, sperm morphology and sperm ratio in wild-type and X-ray irradiated individuals of T. absoluta. The diploid chromosome number of T. absoluta was 2n = 58 including the pair of sex chromosomes: ZZ in males and WZ in females, which were the largest elements of the complement. Irradiation of pupae in an X-ray machine with a dose of 200 Gy generated various types of chromosomal rearrangements including translocations and fragmentations, resulting in altered chromosome numbers. The analysis of spermatozoa in T. absoluta revealed a significant morphological difference between apyrene and eupyrene sperm bundles. Irradiation with X-ray doses of 100, 150, 200 and 250 Gy did not have a significant effect on the apyrene to eupyrene sperm ratio. However, males irradiated with 300 Gy produced significantly more apyrene sperm than non-irradiated males. All the doses applied influenced the morphology of eupyrene sperm bundles. The modified eupyrene sperm bundles could be used as a bioindicator during the monitoring of an IS program after the release of irradiated males. We found that the modified eupyrene spermatozoa were transferred to the bursae copulatrices of the females. Males treated with 200 Gy transferred a greater proportion of modified eupyrene sperm than untreated males. The results presented herein provide essential information on the cytology of T. absoluta, which is required to evaluate the quality of the released insects, and for better understanding and application of IS against this economically important pest.Fil: Carabajal Paladino, Leonela Zusel. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Ceske Budejovice; República ChecaFil: Ferrari, María Edith. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas; ArgentinaFil: Lauría, Juan P.. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Genética; ArgentinaFil: Cagnotti, Cynthia Lorena. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Microbiología y Zoología Agrícola; ArgentinaFil: Síchová, Jindra. Ceske Budejovice; República Checa. University of South Bohemia; República ChecaFil: López, Silvia Noelí. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Microbiología y Zoología Agrícola; Argentin