Annotation of hypothetical proteins orthologous in Pongo abelii and Sus scrofa

A hypothetical protein is predicted to be expressed from an open reading frame without known experimental evidence of translation. They constitute a substantial fraction of proteomes. Domain extraction from these hypothetical sequences helps to search for protein coding genes for protein structural and functional annotation. We describe the analysis of prediction data in a sequence dataset of hypothetical protein orthologs of Pongo abelii (orangutan) and Sus scrofa (pig). It should be noted that these orangutan-pig orthologs are also non-homologous to human proteins. These predicted data find application in the genome wide annotation of proteins in poorly understood genomes.

Abbreviations

PDB - Protein Data Bank, DEG - Database of Essential Genes, CDD - Conserved Domain Database, IUCN - International Union for Conservation of Nature.     

De Novo Assembly and Functional Annotation of the Olive (Olea europaea) Transcriptome

Olive breeding programmes are focused on selecting for traits as short juvenile period, plant architecture suited for mechanical harvest, or oil characteristics, including fatty acid composition, phenolic, and volatile compounds to suit new markets. Understanding the molecular basis of these characteristics and improving the efficiency of such breeding programmes require the development of genomic information and tools. However, despite its economic relevance, genomic information on olive or closely related species is still scarce. We have applied Sanger and 454 pyrosequencing technologies to generate close to 2 million reads from 12 cDNA libraries obtained from the Picual, Arbequina, and Lechin de Sevilla cultivars and seedlings from a segregating progeny of a Picual × Arbequina cross. The libraries include fruit mesocarp and seeds at three relevant developmental stages, young stems and leaves, active juvenile and adult buds as well as dormant buds, and juvenile and adult roots. The reads were assembled by library or tissue and then assembled together into 81 020 unigenes with an average size of 496 bases. Here, we report their assembly and their functional annotation.     

Introduction of two chromosomal translocations of Sus scrofa nigripes and Sus scrofa scrofa into the genome of Sus scrofa domestica

Summary Hybrids between wild and domestic pigs with two types of translocations in the karyotype were studied. The translocations of type I were first detected in a population of the Middle Asian wild boars. Type II was identified in a populations of the Central European subspecies. A large number of Middle Asian and Central European hybrids and their F₁-F₃ hybrids from crosses with domestic pigs were viable. By means of differential chromosome staining, the mechanism of the formation of synthetic karyotypes, as well as some features of translocation inheritance, were established.The introduction of two translocations into a single genome and the same chromosome set of these hybrids not only modified chromosome number, but also the composition of the linkage groups. The hybrids heterozygous for two translocations and their hybrid progeny are characterized by an obligatory heterozygozity for a large number of genes, gene complexes and linked genes. It is suggested that this heterozygozity may be associated with heterotic events. The use of such hybrids in pig breeding may provide heterosis for viability and productivity.     

Grouping-patterns and inter-group relationships of Japanese wild boars (Sus scrofa leucomystax) in the Rokko mountain area

Grouping-patterns and inter-group relationships of Japanese wild boars (Sus scrofa leucomystax) were studied at a provisioning site in the Rokko mountain area, Hyogo Prefecture, Japan, from 1982 to 1983. The observations were divided into four study periods. Almost all wild boars were individually identified and their kin-relationships were followed from the beginning of the study. To examine grouping-patterns of Japanese wild boars, the degree of association between any two individuals, based on coexisting time at the provisioning site, was analyzed for each study period. Mother and her litter group (MLG), female littermate group (FLG) and solitary individual were recognized grouping-patterns. Groups did not associate with each other. Male offspring separated from their mother before 1 year of age and become solitary. Separation of female offspring occurred before the subsequent parturition of their mother. The proximate cause of separation was increased aggression by the mother. After separation, female offspring formed a FLG. However, the FLG seemed to be generally a temporary one, maintaining its stability only until parturition of it's members. Thereafter adult females had no close association with any other individuals, except for their own infants. Male offspring disappeared from their natal area, while female offspring could remain there.     

The sexual function of wallowing in male wild boar (Sus scrofa)

The wild boar (Sus scrofa) is a medium-sized ungulate that produces a large variety of marks. Traditionally, wallowing is an activity that has fundamentally been related to several processes such as thermoregulation, reduction in the number of ectoparasites or disinfection of wounds in the skin of males resulting from fights to reach females. In this study, I analysed another possible function of wallowing in free-ranging wild boar populations when temperatures are low and parasitic numbers are not significant. The results indicate that during the sampling time, from October to February, the number of wild boars with a mud layer on their skin was 47, out of a total of 558 wild boar analysed. Of these 47 wild boars, 44 were males and within this group, 40 individuals were adult males. The wallowed males were bigger and older than non-wallowed males hunted at the same time. In addition, I found that males wallowed mainly during autumn (90.9% of all cases). In the total number of wild boars analysed, I did not notice individuals with wounds resulting from fights other than from the hunting day. On the other hand, the analysis of the females reproductive systems indicated that the rut period took place during the last days of October and the first days of November. From these results, the coincidence of the rut period with the maximum of wallowing in adult males could be indicative of a sexual function of this activity.     

Annual and seasonal space use of different age classes of female wild boar Sus scrofa L.

In a radiotelemetric study, we analysed space use of 24 female specimens (14 family groups and 14 nonreproductive yearling females) out of 23 wild boar groups for periods between 3 and 39 months. Generally, wild boar used relatively small areas, showed high site fidelity but also a strong individual variation of home ranges, indicating a high flexibility in space use. Although age-specific differences were not statistically significant, female yearlings tended to have larger mean annual home ranges (1,185 ha MCP) than animals ranging in family groups (771 ha). Yearlings also showed a stronger shifting from spring to summer home ranges (2,345 m) and a tendency towards larger home range sizes in summer (791 ha MCP), compared to family groups (shift 1,766 m, MCP 461 ha). Yearlings displayed a dislocation of about 1 km of the annual centre in the first year after dividing from the mother. In contrast, in adults older than 2 years, the dislocation of the annual center was only 240 m.     

Habitat and reproductive phenology of wild boar (Sus scrofa) in the western Iberian Peninsula

We examined the reproductive phenology of wild boar populations in four regions of the western Iberian Peninsula during the 1999/2000 hunting season (October–February). To estimate conception dates and birth distribution frequencies, we used foetal weights. Regions differed significantly, and we detected a relationship between region and birth distribution frequencies. Throughout the year, food availability had a major influence on the distribution of farrowing. Although a short period of high food availability leads to highly synchronous births, even in relatively harsh environmental conditions, adult females that exploit low-quality food items appear to be able to give birth at any time of the year.     

四川山鹧鸪的转录组组装和注释

四川山鹧鸪Arborophila rufipectus是中国特有的珍稀濒危鸟类.本研究对1只成年雄性四川山鹧鸪个体的心脏、肝脏和肾脏进行了转录组测序、组装和注释.其原始序列过滤后分别产生了5.70 G、4.60 G和5.16 G数据.286661条转录本经过Trinity组装并去掉冗余后共得到234488个基因.BUS...     

Investigations on the radiocaesium contamination of wild boar (Sus scrofa) meat in Rhineland-Palatinate: a stomach content analysis

To substantiate the pathways of radiocaesium contamination in wild boars in parts of Rhineland-Palatinate, we analysed radiocaesium-activityconcentration of 2,433 wild boars shot in an area covering 45,400 ha in the western part of the Palatinate Forest between January 2001 and February 2003. Also, for a fraction of 689 animals shot between May 2002 and February 2003, we collected their stomachs for the examination of content and Cs-activity concentration. Wild boar meat contamination followed a seasonal curve with maximum proportions exceeding accepted levels in the summer (21–26%) and minimum levels in winter (1–9.3%) indicating a higher consumption of a contaminating source during the vegetation period. The autumn decline is obviously attributed to the extensive consumption of low-contaminated beech nuts. An exact analysis of food composition in 18 stomachs with maximum Cs-activity concentrations [345–1,749 Bq/kg (fresh matter: fm)] and 18 with low Cs-activity concentrations (20–199 Bq/kg) was carried out in the summer of 2002. Deer truffles (Elaphomyces granulatus) were found in significantly higher proportions in stomachs with maximum contamination levels than in stomachs with lowcontamination levels. This fungus was found in the Palatinate Forest, by a trained dog, in average densities of 1 truffel/20 m² primarily in spruce stands, showing an average Cs-concentration of 6,030 Bq/kg (fm). On the basis of our findings we stress the hypothesis that deer truffles function as a main Cs-source for the wild boar in Rhineland-Palatinate.     

Unravelling the complexity of domestication: a case study using morphometrics and ancient DNA analyses of archaeological pigs from Romania

Current evidence suggests that pigs were first domesticated in Eastern Anatolia during the ninth millennium cal BC before dispersing into Europe with Early Neolithic farmers from the beginning of the seventh millennium. Recent ancient DNA (aDNA) research also indicates the incorporation of European wild boar into domestic stock during the Neolithization process. In order to establish the timing of the arrival of domestic pigs into Europe, and to test hypotheses regarding the role European wild boar played in the domestication process, we combined a geometric morphometric analysis (allowing us to combine tooth size and shape) of 449 Romanian ancient teeth with aDNA analysis. Our results firstly substantiate claims that the first domestic pigs in Romania possessed the same mtDNA signatures found in Neolithic pigs in west and central Anatolia. Second, we identified a significant proportion of individuals with large molars whose tooth shape matched that of archaeological (likely) domestic pigs. These large ‘domestic shape’ specimens were present from the outset of the Romanian Neolithic (6100–5500 cal BC) through to later prehistory, suggesting a long history of admixture between introduced domestic pigs and local wild boar. Finally, we confirmed a turnover in mitochondrial lineages found in domestic pigs, possibly coincident with human migration into Anatolia and the Levant that occurred in later prehistory.     

Seroprevalence of Trichinella sp. in Wild Boars (Sus scrofa) from Yanggu-gun,Gangwon-do,Korea

A total 7 outbreaks of trichinellosis have occurred in Korea, mostly as a result of consumption of raw wild boar (Sus scrofa) meat. Since only 1 serological survey on wild boars had yet been performed in Korea, the present study aimed to estimate the prevalence of trichinellosis in wild boars and some species of rodents by artificial digestion and serological examinations in Yanggu-gun, Gangwon-do, the endemic area of trichinellosis. Both the wild boar and rodent muscle samples revealed no Trichinella larvae by direct examination and artificial digestion method. However, serological examinations revealed that 4 wild boar sera samples out of 118 (3.4%) were positive to Trichinella antigen. Although the recovery of Trichinella larvae ended in a failure, it is proved for the first time that the sylvatic cycle of Trichinella has been maintained in wild boars of Gangwon-do, Korea.     

Spargana in a Weasel,Mustela sibirica manchurica,and a Wild Boar,Sus scrofa,from Gangwon-do,Korea

To know the status of sparganum (plerocercoid of Spirometra erinacei) infection in the Korean wild life, several species of wild animals were captured in Gangwon-do and examined for their status of infection with spargana. From February to December 2011, a total of 62 wild boars, 5 badgers, 1 weasel, 1 Siberian chipmunk, and 53 wild rodents were captured, and their whole muscles were examined with naked eyes for the presence of spargana worms. From the weasel and 1 wild boar, a total of 5 spargana specimens were extracted. The weasel was for the first time recorded as an intermediate or paratenic/transport host of S. erinacei in Korea, and both the weasel (Mustela sibirica manchurica) and wild boar (Sus scrofa) were added to the list of wild animals carrying spargana.     

Genomic Resources for Gene Discovery,Functional Genome Annotation,and Evolutionary Studies of Maize and Its Close Relatives

Maize is one of the most important food crops and a key model for genetics and developmental biology. A genetically anchored and high-quality draft genome sequence of maize inbred B73 has been obtained to serve as a reference sequence. To facilitate evolutionary studies in maize and its close relatives, much like the Oryza Map Alignment Project (OMAP) (www.OMAP.org) bacterial artificial chromosome (BAC) resource did for the rice community, we constructed BAC libraries for maize inbred lines Zheng58, Chang7-2, and Mo17 and maize wild relatives Zea mays ssp. parviglumis and Tripsacum dactyloides. Furthermore, to extend functional genomic studies to maize and sorghum, we also constructed binary BAC (BIBAC) libraries for the maize inbred B73 and the sorghum landrace Nengsi-1. The BAC/BIBAC vectors facilitate transfer of large intact DNA inserts from BAC clones to the BIBAC vector and functional complementation of large DNA fragments. These seven Zea Map Alignment Project (ZMAP) BAC/BIBAC libraries have average insert sizes ranging from 92 to 148 kb, organellar DNA from 0.17 to 2.3%, empty vector rates between 0.35 and 5.56%, and genome equivalents of 4.7- to 8.4-fold. The usefulness of the Parviglumis and Tripsacum BAC libraries was demonstrated by mapping clones to the reference genome. Novel genes and alleles present in these ZMAP libraries can now be used for functional complementation studies and positional or homology-based cloning of genes for translational genomics.     

New data in France on the trematode Alaria alata (Goeze, 1792) obtained during Trichinella inspections

The trematode Alaria alata is a cosmopolite parasite found in red foxes (Vulpes vulpes), the main definitive host in Europe. In contrast only few data are reported in wild boars (Sus scrofa), a paratenic host. The aim of this paper is to describe the importance and distribution of Alaria alata mesocercariae in wild boars, information is given by findings of these larvae during Trichinella mandatory meat inspection on wild boars' carcasses aimed for human consumption. More than a hundred cases of mesocercariae positive animals are found every year in the East of France. First investigations on the parasite's resistance to deep-freezing in meat are presented in this work.