Biomolecules

Journal Browser

► Journal Browser

Special Issue Editor

Special Issue Information

Dear Colleagues,

Following a very successful first edition, we are pleased to announce the launch of a second edition of the Special Issue on "The Genomics Era: From Reference Genomes to Pan-Genomic Graphs".

Since entering the "genomic era", up to now, the scientific community has relied on a single "reference" genome for each species, used as the basis for a wide range of genetic analyses. With the number of sequenced genomes steadily increasing, the concept of "reference" genomes has been reconsidered; presently, the idea of using a "pangenome" to describe the complete set of variations in a species appears promising.

This Special Issue of Biomolecules focuses on new insights that pangenomic analyses have brought into a wide range of topics, from microbiology and virology to human genetics, as well as the exploration of pangenomics’ potential in aiding human disease diagnostics.

Studies that investigate pan-genome profiles by defining core genomes up to the reconstruction of accessory genomes across multiple organisms are welcome, as well as those that impliment computational pangenomic approaches and novel statistical methods to highlight the presence of the signature of selection at the genome level. The topics of interest range include metagenomics, illustrating core or dispensable genes potentially related to microbial pathogenicity or niche adaptation; pan-transcriptomics used for a more compact representation of transcriptomes; and human genetics based on linking whole-genome variations to human diversity, diseases, and other related topics.

Both research (in particular) and review articles proposing novelties or overviews, respectively, are welcome.

Prof. Dr. Chiara Scapoli
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Related Special Issue

Published Papers (1 paper)

Research

16 pages, 5491 KiB

Open AccessArticle

In-Depth Genome Characterization and Pan-Genome Analysis of Strain KMM 296, a Producer of Highly Active Alkaline Phosphatase; Proposal for the Reclassification of Cobetia litoralis and Cobetia pacifica as the Later Heterotypic Synonyms of Cobetia amphilecti and Cobetia marina, and Emended Description of the Species Cobetia amphilecti and Cobetia marina

by Olga Nedashkovskaya, Larissa Balabanova, Nadezhda Otstavnykh, Natalia Zhukova, Ekaterina Detkova, Aleksandra Seitkalieva, Evgenia Bystritskaya, Yulia Noskova, Liudmila Tekutyeva and Marina Isaeva

Biomolecules 2024, 14(2), 196; https://doi.org/10.3390/biom14020196 - 06 Feb 2024

Cited by 1 | Viewed by 856

Abstract

A strictly aerobic, Gram-stain-negative, rod-shaped, and motile bacterium, designated strain KMM 296, isolated from the coelomic fluid of the mussel Crenomytilus grayanus, was investigated in detail due to its ability to produce a highly active alkaline phosphatase CmAP of the structural family PhoA. A previous taxonomic study allocated the strain to the species Cobetia marina, a member of the family Halomonadaceae of the class Gammaproteobacteria. However, 16S rRNA gene sequencing showed KMM 296’s relatedness to Cobetia amphilecti NRIC 0815^T. The isolate grew with 0.5–19% NaCl at 4–42 °C and hydrolyzed Tweens 20 and 40 and L-tyrosine. The DNA G+C content was 62.5 mol%. The prevalent fatty acids were C_18:1 ω7c, C_12:0 3-OH, C_18:1 ω7c, C_12:0, and C_17:0 cyclo. The polar lipid profile was characterized by the presence of phosphatidylethanolamine, phosphatidylglycerol, phosphatidic acid, and also an unidentified aminolipid, phospholipid, and a few unidentified lipids. The major respiratory quinone was Q-8. According to phylogenomic and chemotaxonomic evidence, and the nearest neighbors, the strain KMM 296 represents a member of the species C. amphilecti. The genome-based analysis of C. amphilecti NRIC 0815^T and C. litoralis NRIC 0814^T showed their belonging to a single species. In addition, the high similarity between the C. pacifica NRIC 0813^T and C. marina LMG 2217^T genomes suggests their affiliation to one species. Based on the rules of priority, C. litoralis should be reclassified as a later heterotypic synonym of C. amphilecti, and C. pacifica is a later heterotypic synonym of C. marina. The emended descriptions of the species C. amphilecti and C. marina are also proposed. Full article

(This article belongs to the Special Issue The Genomics Era: From Reference Genomes to Pan-Genomic Approach II)

► Show Figures