Clitarchus transcriptome assembly from five different tissues

Transcriptome assembly constructed from C. hookeri female antennae, head and prothorax, midgut, leg and male terminalia. More details are shown in ReadMe file

Faktory ovlivňující reprodukční ukazatele dojnic ve vybraném chovu holštýnského skotu

The diploma thesis dealt with the analysis, and evaluation of dairy performance and its correlation with reproductive rates of Holstein cattle. Milk cows which were kept in Měcholupy agricultural, Inc., Předslav were analyzed between 2013 - 2015. Th ecompany is located in the foothills of the Bohemian Forest (Šumava). It breeds cattle for milk as well as meat, and pigs. The company management is committed to achieve good levels of milk production. It pays constant attention to this issue, so the average performance has risen since 2013 from 8 726 kilograms of milk to 9 093 kg of milk per cow in 2015. Cows on the 4th and higher lactation reached the highest performance in 2015 9 649 kg of milk. As for the European Union who abolished milk quotas in 2015 and the situation on the milk market is still complicated by banning exports of milk powder to Russia (Russian annexation of the Crimea), the management´s effort has been to produce milk at the lowest possible cost. They keep trying to limit culling as much as possible, so that they solve the problem of mastitis and reproduction at the highest level. Each cow which is treated has an individual approach, as well as the animal husbandry has specific requirements for animal breeding company in terms of quality seed. The results showed that milk cows with other health problems were eliminated the most (38.6% per year from 2013 to 2015) and also the ones with metabolism disorders and problems with hooves. The mastitis issue is dealt with very effectively, so that it is not one of the major problems of the herd (7.24 % for 2013 -2015). Management seeks to eliminate the problem milk cow in the lowest age and conversely on contrary if the animal is healthy, they try to keep it in the herd as long as possible, because such an animal has the greatest economic effect. Reproductive rateis not too satisfactory, but the management has no interest in hormonal control of reproduction. Active search of rutting cows is preferred by nursing staff. They cooperate actively with animal breeders and require a delivery of the insemination doses according to their requirements for each for each co

Additional file 2: of Evolution of neuropeptides in non-pterygote hexapods

Sequence logos of single-copy peptides. The logos show the sequence variability in the single-copy peptides (<30 amino acids) of non-pterygote hexapod lineages determined using WebLogo version 2.8.2 (http://weblogo.berkeley.edu/). For species with two described genes containing different mature neuropeptides, the more conserved sequence was selected. CNMa was not found in Protura and Collembola, while elevenin was not found in Collembola. Pigment-dispersing factor (PDF) was not found in Protura and Diplura. For comparative purposes, the sequence conservation of CAPA-PVK paracopies was added as an example of multiple-copy peptides. A distinct core sequence is obvious in all sequence logos. The N-terminal sequence motifs are variable in a number of peptides, including SIFa, and this variability is similar to that of the N-termini in the different PVK paracopies. (DOC 460 kb

Additional file 1: of Functional characterization of the Hyles euphorbiae hawkmoth transcriptome reveals strong expression of phorbol ester detoxification and seasonal cold hardiness genes

Figure S1. Percentage and number (in bars) of annotated transcripts. This is of a total of 18,080 transcripts with a cut-off of e = 10− 5 and 55% sequence similarity. BLASTX hits include GO term annotated hits. Those include KEGG hits, which in turn consist of transcripts annotated with enzyme codes and respective metabolic pathways. (JPEG 392 kb

Additional file 7: of Functional characterization of the Hyles euphorbiae hawkmoth transcriptome reveals strong expression of phorbol ester detoxification and seasonal cold hardiness genes

Table S3. Table of 389 detoxification related differentially expressed H. euphorbiae tags. Assignment with BLASTN transcript hits and annotated protein sequence descriptions (nr protein database version 09/2016). (XLSX 152 kb

Additional file 6: of Functional characterization of the Hyles euphorbiae hawkmoth transcriptome reveals strong expression of phorbol ester detoxification and seasonal cold hardiness genes

Figure S4. Distribution of DeepSuperSAGE tag frequencies and p-value vs. fold change (FC) of tags. Left panel: Normalized tag counts per million tags (tpm) in treatment and control libraries. Right panel: Relationship between tag FC (ratio of tpm counts) and p-value of significance. Up- and down-regulated tags (p < 10− 10, − 1 > Log2FC > 1) are marked in red and green, respectively. Of those, the best BLASTN hits to a transcript, according to bit score and e-value, were used to assess the transcript expression value. (a) cooled (C) vs. uncooled (UC) library. (b) TPA treated (T) vs. untreated (UT) library. (ZIP 946 kb

Additional file 3: of Functional characterization of the Hyles euphorbiae hawkmoth transcriptome reveals strong expression of phorbol ester detoxification and seasonal cold hardiness genes

Figure S2. Distribution of species names among BLAST hits. The 20 most frequent species names affiliated with best BLASTX hits against nr are shown, making up (a) 8626 transcripts among the entire annotated H. euphorbiae assembly, and (b) 8219 (95%) among Lepidoptera matches only. (ZIP 259 kb

Additional file 9: of Functional characterization of the Hyles euphorbiae hawkmoth transcriptome reveals strong expression of phorbol ester detoxification and seasonal cold hardiness genes

Table S5. Details of enriched GO terms among differentially expressed transcripts. GO terms (biological process and molecular function) are grouped according to REVIGO semantic categories and generic GO slim terms. (DOC 145 kb

Additional file 8: of Functional characterization of the Hyles euphorbiae hawkmoth transcriptome reveals strong expression of phorbol ester detoxification and seasonal cold hardiness genes

Table S4. Table of 605 cold related differentially expressed H. euphorbiae tags. Assignment with BLASTN transcript hits and annotated protein sequence descriptions (nr protein database version 09/2016). (XLSX 169 kb

Additional file 4: of Functional characterization of the Hyles euphorbiae hawkmoth transcriptome reveals strong expression of phorbol ester detoxification and seasonal cold hardiness genes

Table S2. List of 125 KEGG pathways and 513 different enzyme codes. Enzyme commission numbers (EC) and KEGG pathways are given; to which 2806 BLAST annotated H. euphorbiae transcripts have been mapped. (XLSX 53 kb