Database indexing for production MegaBLAST searches

Motivation: The BLAST software package for sequence comparison speeds up homology search by preprocessing a query sequence into a lookup table. Numerous research studies have suggested that preprocessing the database instead would give better performance. However, production usage of sequence comparison methods that preprocess the database has been limited to programs such as BLAT and SSAHA that are designed to find matches when query and database subsequences are highly similar

Annotation of Bacteriophage BigPaolini

Bacteriophages were discovered nearly 100 years ago. With new interest in phages many phages are being analyzed and annotated to understand the diversity within the phage world.https://digitalcommons.mtech.edu/urp_aug_2018/1010/thumbnail.jp

Bacterial Characterization of Sourdough from a Local Factory

Motivation: Sourdough is the fermentation product of flour and water dough by yeasts and lactic acid bacteria (LAB). Depending on the origin of the microorganisms it can be classified in Type I (spontaneous and with backslopping), Type II (uses a starter culture without backslopping) and Type III (uses a starter culture and backslopping)1. Sourdough-based products have improved properties, which have been attributed to the LAB and their metabolism 2. This study is focused on the characterization of LAB in an industrial sourdough at two different moments. Methods: To isolate LAB from sourdough, independent samples were taken from a homogenized portion. Appropriate dilutions were plated on mMRS agar and grown on aerobiosis at 30ºC. Cell concentration was calculated as CFU/g of sourdough.  Morphologies of Catalase negative isolates were determined by optic microscopy. For molecular identification, DNA was extracted by a method described by Cold Spring Harbour Laboratory3. Fragments from rRNA 16S gene were amplified by PCR and sent for sequencing. Sequences were compared with databases using the BLASTn tool4. Non-pathogen S. aureus and L. innocua were used as indicator strains to detect antimicrobial capacity on BHI medium. Clear zones around colonies were rated as positive results. Results: LAB were present in the two sourdough samples at 2.75*10^7 CFU/g and 4.3*10^7 CFU/g. The dominant morphologies were long, medium and short bacilli. They presented percentages of 41.5%, 18.9% and 39.6% in the first sample and 13.5%, 30.8% and 55.8% in the second, respectively. The dominant species were Lactobacillus crustorum (corresponding to long bacilli), Lb. rossiae (short bacilli) and Lb. plantarum (medium bacilli). Antagonistic activity was detected only against S. aureus just in 5% of candidates from the second sample. Conclusions: LABs present in two sourdough sample´s from the same factory have been characterized. Cell concentrations were similar to that described in the bibliography. Dominant species identified were Lb. crustorum, Lb. rossiae and Lb. plantarum. However, their proportion was different in the two sourdough samples. Antagonistic activity against S. aureus was detected in the second sampl

Draft genome sequence of Xanthomonas arboricola pv. pruni strain Xap33, causal agent of bacterial spot disease on almond

We report the annotated genome sequence of Xanthomonas arboricola pv. pruni strain Xap33, isolated from almond leaves showing bacterial spot disease symptoms in Spain. The availability of this genome sequence will aid our understanding of the infection mechanism of this bacterium as well as its relationship to other species of the same genus.Publishe

Evidence of Massive Horizontal Gene Transfer Between Humans and Plasmodium vivax

The horizontal transfer of DNA between different organisms is a major force shaping the genomes of prokaryotes, but is considered to have a minor role in eukaryotes, with only a handful of known examples, mostly of limited size. The nucleotide databases of Plasmodium genomes were divided into small fragments and compared to human, as well as to other Plasmodium genomes. This computational approach revealed that the Plasmodium vivax genome is interlaced with multiple DNA fragments that were likely acquired via horizontal transfer from humans. Contamination is a major concern in such studies; moreover, it must be determined if the identified homologies might be due to chance. These reservations are supported by the fact that the identified homologous sequences were found to be predominantly within short contigs. Re-sequencing of candidate sites using distinct isolations of P. vivax genomic DNA showed deletions not found in the human genome, and with much greater similarity to the P. vivax than human genome. Moreover, the identified fragments were enriched for mRNA coding sequences and genes that are known to be functionally important for P. vivax, including nitric oxide synthase 1 (neuronal) adaptor and Interleukin-1 family, suggesting a functional role. These results are important for two reasons. First, a directional massive horizontal transfer of genetic material from humans to another eukaryote is shown for the first time. This sheds light on parasite evolution, co-adaptation and immune evasion. Second, the DNA found is enriched for Interleukin-1 family, which is known to be essential for malaria protection. This indicates a functional role and might serve to better understand how Plasmodium vivax and the immune system interact

The identification of a novel, high frequency variant in the Cytochrome b gene in an isolated population of a rare fish, Spined Loach Cobitis taenia, in England: A population worth protecting?

The spined loach Cobitis taenia, is listed as a protected species under Appendix 3 of the Bern Convention and Annex II of the European Council Directive (92/43/EEC) on the conservation of natural habitats and of wild fauna and flora. It is desirable therefore to understand the genetic diversity within European populations. In a molecular genetic analysis of the cytochrome b gene in Cobitis taenia from three sites in the upper reaches of the River Trent catchment, a novel high frequency variant was identified which has not been previously reported in any European or Non-European population

USING SHORT SEQUENCE matK GENE AS BARCODE DNA FOR IDENTIFICATION OF DURIO Sp IN TERNATE ISLAND

The Barcode of Life Consortium (CBOL) recommended a standard method for the identification of plant species using matK and rbcL barcoding gene. This study was aimed to evaluate the efficiency of matK DNA barcoding for identification of local durian (Durio sp.) from Ternate Island. Total 15 local durian has been used in this study. Whole genom DNA was isolated by Geneid plant DNA kit and then successfully amplified by the Polymerase Chain Reaction (PCR) technique using specific primer. MatK successfully amplified with 245 bp in length. MatK has sequencing success (71.3%) and relative high of Quality value 20+ (86%). BLAST analysis of the sequence showed that local durian in Ternate are identifies as Durio zibethinus and Neesia malayana with query cover 97%-99%. It could be concluded that matK with short sequence is not efficience for durian identification.  The recommended  in this studies  for using of molecular markers with sequence lengths above 500 bp would be more effective for the identification of cryptic species Durio sp. and other

Molecular Phylogenetic of Cerithidea anticipata (Iredale, 1929) (Mollusk: Gastropod)

Species identification is very important and an important part of bioecological studies, so phylogenetic studies of Cerithidea anticipata (Iredale, 1929) was conducted in September 2020 to identify C. anticipata (Iredale, 1929) based on DNA barcoding techniques. Samples of C. anticipata (Iredale, 1929) were collected from the mangrove ecosystem of Payum Merauke Beach Papua (Indonesia), where the genes used were primary COI Gene forward LCO1490 and reverse HCO2198. The result of DNA amplification obtained DNA sequence length of 660 bp, then based on the identification of Basic Local Alignment Search Tools (BLAST) obtained a similarity level of 98.42% and phylogenetic reconstruction showed the existence of grouping based on the degree of similarity and genetic distance between populations.Keywords: Cerithidea anticipata; COI genes; DNA barcoding; phylogeneticsAbstrakIdentifikasi spesies sangat penting dilakukan dan menjadi bagian penting dalam studi bioekologi, sehingga kajian filogenetik Cerithidea anticipata (Iredale, 1929) telah dilakukan pada bulan September 2020 dengan tujuan untuk mengidentifikasi C. anticipata (Iredale, 1929) berdasarkan teknik DNA barcoding. Sampel C. anticipata (Iredale, 1929) dikoleksi dari ekosistem mangrove Pantai Payum Merauke Papua (Indonesia), dimana gen yang digunakan adalah Gen COI primer forward LCO1490 dan reverse HCO2198. Hasil dari amplifikasi DNA diperoleh panjang sekuen DNA 660 bp, kemudian berdasarkan identifikasi Basic Local Alignment Search Tools (BLAST) diperoleh tingkat kemiripannya 98.42% dan rekonstruksi filogenetiknya memperlihatkan adanya pengelompokan berdasarkan tingkat kemiripan maupun jarak genetik antar populasi.Kata kunci: Cerithidea anticipata; Gen COI; DNA barcoding; filogeneti

Construction of two whole genome radiation hybrid panels for dromedary (Camelus dromedarius): 5000RAD and 15000RAD

The availability of genomic resources including linkage information for camelids has been very limited. Here, we describe the construction of a set of two radiation hybrid (RH) panels (5000RAD and 15000RAD) for the dromedary (Camelus dromedarius) as a permanent genetic resource for camel genome researchers worldwide. For the 5000RAD panel, a total of 245 female camel-hamster radiation hybrid clones were collected, of which 186 were screened with 44 custom designed marker loci distributed throughout camel genome. The overall mean retention frequency (RF) of the final set of 93 hybrids was 47.7%. For the 15000RAD panel, 238 male dromedary-hamster radiation hybrid clones were collected, of which 93 were tested using 44 PCR markers. The final set of 90 clones had a mean RF of 39.9%. This 15000RAD panel is an important high-resolution complement to the main 5000RAD panel and an indispensable tool for resolving complex genomic regions. This valuable genetic resource of dromedary RH panels is expected to be instrumental for constructing a high resolution camel genome map. Construction of the set of RH panels is essential step toward chromosome level reference quality genome assembly that is critical for advancing camelid genomics and the development of custom genomic tools