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Iskalni niz: "ključne besede" (genome) .

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The Carniolan honeybee from Slovenia : a complete and annotated mitochondrial genome with comparisons to closely related Apis mellifera subspecies
Ajda Moškrič, Andraž Marinč, Polonca Ferk, Branimir Leskošek, Mai-Britt Mosbech, Ignas Bunikis, Olga Vinnere Pettersson, Lucile Soler, Janez Prešern, izvirni znanstveni članek

Povzetek: The complete mitochondrial genome of the Carniolan honeybee (Apis mellifera carnica) from Slovenia, a homeland of this subspecies, was acquired in two contigs from WGS data and annotated. The newly obtained mitochondrial genome is a circular closed loop of 16,447 bp. It comprises 37 genes (13 protein coding genes, 22 tRNA genes, and 2 rRNA genes) and an AT-rich control region. The order of the tRNA genes resembles the order characteristic of A. mellifera. The mitogenomic sequence of A. m. carnica from Slovenia contains 44 uniquely coded sites in comparison to the closely related subspecies A. m. ligustica and to A. m. carnica from Austria. Furthermore, 24 differences were recognised in comparison between A. m. carnica and A. m. ligustica subspecies. Among them, there are three SNPs that affect translation in the nd2, nd4, and cox2 genes, respectively. The phylogenetic placement of A. m. carnica from Slovenia within C lineage deviates from the expected position and changes the perspective on relationship between C and O lineages. The results of this study represent a valuable addition to the information available in the phylogenomic studies of A. mellifera—a pollinator species of worldwide importance. Such genomic information is essential for this local subspecies’ conservation and preservation as well as its breeding and selection.
Ključne besede: western honeybee, Apis mellifera carnica, mitochondrial genome, phylogeny, C lineage, annotation, whole genome sequencing, protection, conservation
Objavljeno v DiRROS: 06.09.2022; Ogledov: 155; Prenosov: 74
.pdf Celotno besedilo (1,06 MB)

The era of reference genomes in conservation genomics
Giulio Formenti, 2022, izvirni znanstveni članek

Povzetek: Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics.
Ključne besede: conservation genetics, biodiversity conservation, European Reference Genome Atlas, ERGA
Objavljeno v DiRROS: 03.02.2022; Ogledov: 383; Prenosov: 307
.pdf Celotno besedilo (519,06 KB)
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Genomic insights into the Mycobacterium kansasii complex : an update
Tomasz Jagielski, Paulina Borówka, Zofia Bakuła, Jakub Lach, Błażej Marciniak, Anna Brzostek, Jarosław Dziadek, Mikołaj Dziurzyński, Lian Pennings, Jakobus van Ingen, Marija Žolnir-Dovč, Dominik Strapagiel, 2020, izvirni znanstveni članek

Povzetek: Only very recently, has it been proposed that the hitherto existing Mycobacteriumkansasii subtypes (I–VI) should be elevated, each, to a species rank. Consequently, the former M. kansasii subtypes have been denominated as Mycobacterium kansasii (former type I), Mycobacterium persicum (II), Mycobacterium pseudokansasii (III), Mycobacterium innocens (V), and Mycobacterium attenuatum (VI). The present work extends the recently published findings by using a three-pronged computational strategy, based on the alignment fraction-average nucleotide identity, genome-to-genome distance, and core-genome phylogeny, yet essentially independent and much larger sample, and thus delivers a more refined and complete picture of the M. kansasii complex. Furthermore, five canonical taxonomic markers were used, i.e., 16S rRNA, hsp65, rpoB, and tuf genes, as well as the 16S-23S rRNA intergenic spacer region (ITS). The three major methods produced highly concordant results, corroborating the view that each M. kansasii subtype does represent a distinct species. This work not only consolidates the position of five of the currently erected species, but also provides a description of the sixth one, i.e., Mycobacterium ostraviense sp. nov. to replace the former subtype IV. By showing a close genetic relatedness, amonophyletic origin, and overlapping phenotypes, our findings support the recognition of the M. kansasii complex (MKC), accommodating all M. kansasii-derived species and Mycobacterium gastri. None of the most commonly used taxonomic markers was shown to accurately distinguish all the MKC species. Likewise, no species-specific phenotypic characteristics were found allowing for species differentiation within the complex, except the non-photochromogenicity of M. gastri. To distinguish, most reliably, between the MKC species, and between M. kansasii and M. persicum in particular, whole-genome-based approaches should be applied. In the absence of clear differences in the distribution of the virulence-associated region of difference 1 genes among the M. kansasii-derived species, the pathogenic potential of each of these species can only be speculatively assessed based on their prevalence among the clinically relevant population. Large-scale molecular epidemiological studies are needed to provide a better understanding of the clinical significance and pathobiology of the MKC species. The results of the in vitro drug susceptibility profiling emphasize the priority of rifampicin administration in the treatment of MKC-induced infections, while undermining the use of ethambutol, due to a high resistance to this drug.
Ključne besede: Mycobacteriumkansasii complex, Mycobacteriumostraviense sp. nov., non-tuberculous mycobacteria (NTM), whole genome sequencing, taxonomy
Objavljeno v DiRROS: 31.07.2020; Ogledov: 1431; Prenosov: 1026
.pdf Celotno besedilo (10,22 MB)
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