Genome size evolution in pufferfish: an insight from BAC clone-based Diodon holocanthus genome sequencing

<p>Abstract</p> <p>Background</p> <p>Variations in genome size within and between species have been observed since the 1950 s in diverse taxonomic groups. Serving as model organisms, smooth pufferfish possess the smallest vertebrate genomes. Interestingly, spiny pufferfish from its sister family have genome twice as large as smooth pufferfish. Therefore, comparative genomic analysis between smooth pufferfish and spiny pufferfish is useful for our understanding of genome size evolution in pufferfish.</p> <p>Results</p> <p>Ten BAC clones of a spiny pufferfish <it>Diodon holocanthus </it>were randomly selected and shotgun sequenced. In total, 776 kb of non-redundant sequences without gap representing 0.1% of the <it>D. holocanthus </it>genome were identified, and 77 distinct genes were predicted. In the sequenced <it>D. holocanthus </it>genome, 364 kb is homologous with 265 kb of the <it>Takifugu rubripes </it>genome, and 223 kb is homologous with 148 kb of the <it>Tetraodon nigroviridis </it>genome. The repetitive DNA accounts for 8% of the sequenced <it>D. holocanthus </it>genome, which is higher than that in the <it>T. rubripes </it>genome (6.89%) and that in the <it>Te. nigroviridis </it>genome (4.66%). In the repetitive DNA, 76% is retroelements which account for 6% of the sequenced <it>D. holocanthus </it>genome and belong to known families of transposable elements. More than half of retroelements were distributed within genes. In the non-homologous regions, repeat element proportion in <it>D. holocanthus </it>genome increased to 10.6% compared with <it>T. rubripes </it>and increased to 9.19% compared with <it>Te. nigroviridis</it>. A comparison of 10 well-defined orthologous genes showed that the average intron size (566 bp) in <it>D. holocanthus </it>genome is significantly longer than that in the smooth pufferfish genome (435 bp).</p> <p>Conclusion</p> <p>Compared with the smooth pufferfish, <it>D. holocanthus </it>has a low gene density and repeat elements rich genome. Genome size variation between <it>D. holocanthus </it>and the smooth pufferfish exhibits as length variation between homologous region and different accumulation of non-homologous sequences. The length difference of intron is consistent with the genome size variation between <it>D. holocanthus </it>and the smooth pufferfish. Different transposable element accumulation is responsible for genome size variation between <it>D. holocanthus </it>and the smooth pufferfish.</p

Integrating multi-origin expression data improves the resolution of deep phylogeny of ray-finned fish (Actinopterygii)

The actinopterygians comprise nearly one-half of all extant vertebrate species and are very important for human well-being. However, the phylogenetic relationships among certain groups within the actinopterygians are still uncertain, and debates about these relationships have continued for a long time. Along with the progress achieved in sequencing technologies, phylogenetic analyses based on multi-gene sequences, termed phylogenomic approaches, are becoming increasingly common and often result in well-resolved and highly supported phylogenetic hypotheses. Based on the transcriptome sequences generated in this study and the extensive expression data currently available from public databases, we obtained alignments of 274 orthologue groups for 26 scientifically and commercially important actinopterygians, representing 17 out of 44 orders within the class Actinopterygii. Using these alignments and probabilistic methods, we recovered relationships between basal actinopterygians and teleosts, among teleosts within protacanthopterygians and related lineages, and also within acanthomorphs. These relationships were recovered with high confidence

Complete mitochondrial genomes of the smooth tail nine-spined sticklebacks Pungitius laevis (Gasterosteiformes, Gasterosteidae)

Peer reviewe

Active power decoupling for current source converters:An overview scenario

For single-phase current source converters, there is an inherent limitation in DC-side low-frequency power oscillation, which is twice the grid fundamental frequency. In practice, it transfers to the DC side and results in the low-frequency DC-link ripple. One possible solution is to install excessively large DC-link inductance for attenuating the ripple. However, it is of bulky size and not cost-effective. Another method is to use the passive LC branch for bypassing the power decoupling, but this is still not cost-effective due to the low-frequency LC circuit. Recently, active power decoupling techniques for the current source converters have been sparsely reported in literature. However, there has been no attempt to classify and understand them in a systematic way so far. In order to fill this gap, an overview of the active power decoupling for single-phase current source converters is presented in this paper. Systematic classification and comparison are provided for researchers and engineers to select the appropriate solutions for their specific applications

Construction of Ultradense Linkage Maps with Lep-MAP2 : Stickleback F-2 Recombinant Crosses as an Example

High-density linkage maps are important tools for genome biology and evolutionary genetics by quantifying the extent of recombination, linkage disequilibrium, and chromosomal rearrangements across chromosomes, sexes, and populations. They provide one of the best ways to validate and refine de novo genome assemblies, with the power to identity errors in assemblies increasing with marker density. However, assembly of high-density linkage maps is still challenging due to software limitations. We describe Lep-MAP2, a software for ultradense genome-wide linkage map construction. Lep-MAP2 can handle various family structures and can account for achiasmatic meiosis to gain linkage map accuracy. Simulations show that Lep-MAP2 outperforms other available mapping software both in computational efficiency and accuracy. When applied to two large F-2-generation recombinant crosses between two nine-spined stickleback (Pungitius pungitius) populations, it produced two high-density (similar to 6 markers/cM) linkage maps containing 18,691 and 20,054 single nucleotide polymorphisms. The two maps showed a high degree of synteny, but female maps were 1.5-2 times longer than male maps in all linkage groups, suggesting genome-wide recombination suppression in males. Comparison with the genome sequence of the three-spined stickleback (Gasterosteus aculeatus) revealed a high degree of interspecific synteny with a low frequency (Peer reviewe

Design and Analysis of an Improved Tubular Permanent Magnet Linear Machine with a T-type Magnet Array

The surface-mounted tubular permanent magnet linear machine (SM-TPMLM) is widely used in many industrial applications. However, the PMs are fragile and easily fall off when linear machines are operated at reciprocating oscillation speed over long periods or encounter harsh environments, the exposed PMs are susceptible to corrosion, which reduces the service life of linear machines. To solve this problem, an improved tubular permanent magnet linear machine with a T-type magnet array (T-TPMLM) is proposed. The axial and radial magnets are combined in a magnetic pole array to increase the thrust force, power and protect the PMs. First, an equivalent analytical model of T-TPMLM is established to predict the magnetic field, the subdomain method with Schwarz-Christoffel mapping method is introduced to consider slotting effect and end effect. Then, to verify the merit of the proposed T-TPMLM, a quantitative electromagnetic performance comparison with two traditional SM-TPMLM including radial magnetization and Halbach magnetization is performed through the finite element analysis method (FEM). Besides, the mechanical strength of three linear machines is discussed briefly. Finally, a prototype of proposed T-TPMLM is manufactured and tested to validate the effectiveness of the analytical model and the FEA predicted results. The results show that the proposed machine offers high electromagnetic performance