Coenurosis, caused by the larval coenurus of the tapeworm Taenia multiceps, is a fatal central nervous system disease in both sheep and humans. Though treatment and prevention options are available, the control of coenurosis still faces presents great challenges. Here, we present a high-quality genome sequence of T. multiceps in which 240 Mb (96%) of the genome has been successfully assembled using Pacbio single-molecule real-time (SMRT) and Hi-C data with a N50 length of 44.8 Mb. In total, 49.5 Mb (20.6%) repeat sequences and 13, 013 gene models were identified. We found that Taenia spp. have an expansion of transposable elements and recent small-scale gene duplications following the divergence of Taenia from Echinococcus, but not in Echinococcus genomes, and the genes underlying environmental adaptability and dosage effect tend to be over-retained in the T. multiceps genome. Moreover, we identified several genes encoding proteins involved in proglottid formation and interactions with the host central nervous system, which may contribute to the adaption of T. multiceps to its parasitic life style. Our study not only provides insights into the biology and evolution of T. multiceps, but also identifies a set of species-specific gene targets for developing novel treatment and control tools for coenurosis.

BackgroundAll modern rosids originated from a common hexapolyploid ancestor, and the genomes of some rosids have undergone one or more cycles of paleopolyploidy. After the duplication of the ancient genome, wholesale gene loss and gene subfunctionalization has occurred. Using the extensin super-gene family as an example, we tracked the differential retention and expansion of ancestral extensin genes in four modern rosids, Arabidopsis, Populus, Vitis and Carica, using several analytical methods.ResultsThe majority of extensin genes in each of the modern rosids were found to originate from different ancestral genes. In Arabidopsis and Populus, almost half of the extensins were paralogous duplicates within the genome of each species. By contrast, no paralogous extensins were detected in Vitis and Carica, which have only undergone the common γ-triplication event. It was noteworthy that a group of extensins containing the IPR006706 domain had actively duplicated in Arabidopsis, giving rise to a neo-extensin around every 3 million years. However, such extensins were absent from, or rare in, the other three rosids. A detailed examination revealed that this group of extensins had proliferated significantly in the genomes of a number of species in the Brassicaceae. We propose that this group of extensins might play important roles in the biology and in the evolution of the Brassicaceae. Our analyses also revealed that nearly all of the paralogous and orthologous extensin-pairs have been under strong purifying selection, leading to the strong conservation of the function of extensins duplicated from the same ancestral gene.ConclusionsOur analyses show that extensins originating from a common ancestor have been differentially retained and expanded among four modern rosids. Our findings suggest that, if Arabidopsis is used as the model plant, we can only learn a limited amount about the functions of a particular gene family. These results also provide an example of how it is essential to learn the origination of a gene when analyzing its function across different plant species.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-612) contains supplementary material, which is available to authorized users.

In this study, single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) in the genome of Ziziphus jujuba were identified using sequences generated by the Roche 454 GS-FLX sequencer. A total of, 573,141 reads were produced with an average read length of 360 bp. After quality control, 258,754 of the filtered reads were assembled into 23,864 contigs, and 293,458 remained as singletons. Using the contig assemblies as a reference, 17,160 SNPs and 478 InDels were identified. Among the SNPs, transitions occurred three times more frequently than transversions. In transitions, the number of C/T and G/A transitions was similar. Among the transversions, A/T was the most abundant, and C/G was much rarer than any of the other types of transversions, accounting for only about half the numbers of A/C, A/T and G/T transversions. For the InDels, mononucleotide changes amounted to 64.4% of the total number of InDels. In general, the frequency of detected InDels decreased as the length of the InDels increased. This study provides valuable marker resources for future genetic studies of Ziziphus spp.

In this study, 43 elite clones of Populus deltoides were fingerprinted with ABI 3730 capillary electrophoresis by using six SSR primer pairs. Based on the fingerprinting profiles, 62 polymorphic bands were generated with a mean number of 10 alleles per locus, and allele numbers amplified by each primer in these clones ranged from 5 (NJFUP-poly10) to 16 (NJFUP-poly07). The power of discrimination values for these primer pairs ranged from 0.80 to 0.94, with an average value of 0.89. Among the six primer pairs, the most efficient primer pair for genetic discrimination of these elite clones was NJFUP-poly02, which could identify 22 of the 43 elite clones directly. In conclusion, all the 43 elite clones of P. deltoides could be discriminated unambiguously based on their genotypes at the six SSR loci. The combination of all six loci gave considerable reliability and accuracy for genetic identification of these clonal accessions. Subsequently, genetic relationship of these clones was plotted by the UPGMA clustering and principle component analysis. Results of both analyses indicated that clone "C7-1" had the largest genetic distance from the other clones, followed by clone "C51-1" and a subgroup comprising clone "C100-3" and "C62-3". These clones are proposed to be possibly more affected by the inter-specific gene introgression.Key words: Populus deltoides, clone identification, SSR fingerprinting, UPGMA cluster, PCA plot.Résumé : Dans cette étude, 43 clones élite de Populus deltoides ont été marqués avec six paires d'amorces SSR par électrophorèse capillaire au moyen d'un appareil ABI 3730. D'après la cartographie peptidique, la technique aboutit à 62 bandes polymorphes comprenant en moyenne 10 allèles par locus, le nombre d'allèles amplifiés dans chaque amorce variant de 5 (NJFUP-poly10) à 16 (NJFUP-poly07) chez les clones. La valeur discriminatoire des paires d'amorces variait de 0,80 à 0,94, pour une moyenne de 0,89. Sur les six paires d'amorces, celle permettant la meilleure discrimination génétique des clones élite était NJFUP-poly02, puisqu'elle a permis d'identifier directement 22 clones sur les 43. En conclusion, on est parvenu à distinguer sans ambiguïté les 43 clones élite de P. deltoides d'après leur génotype aux six locus SSR. Combiner les six locus rend l'identification génétique extrêmement fiable et précise pour ces obtentions, issues du clonage. Par la suite, les liens génétiques entre les clones ont été tracés après regroupement par la méthode des moyennes par paire non pondérée (UPGMA) et l'analyse en composantes principales. Dans les deux cas, les résultats indiquent que le clone C7-1 est génétiquement le plus éloigné des autres. Suivaient le clone C51-1 et un sous-groupe composé des clones C100-3 et C62-3. Il se peut que ces clones soient plus affectés par l'introgression des gènes interspécifiques. [Traduit par la Rédaction]