The complete mitochondrial genome of the red-footed tortoise (Chelonoidis carbonarius Spix 1824).

In this study, we report the complete mitochondrial genome of the red-footed tortoise (Chelonoidis carbonarius). The compete mitochondrial genome of C. carbonarius is 16,639 bp in length, including 13 protein-coding genes, 22 tRNA genes, and two rRNA genes. The mitogenome was deposited in NCBI GenBank under the accession number OQ789392. Furthermore, we also constructed a phylogenetic tree of Chelonoidis using eight species. These results will aid the conservation of Chelonoidis from the perspective of genetic evolution.

Evolutionary Principles of Bacterial Signaling Capacity and Complexity.

Microbes rely on signal transduction systems to sense and respond to environmental changes for survival and reproduction. It is generally known that niche adaptation plays an important role in shaping the signaling repertoire. However, the evolution of bacterial signaling capacity lacks systematic studies with a temporal direction. In particular, it is unclear how complexity evolved from simplicity or vice versa for signaling networks. Here, we examine the evolutionary processes of major signal transduction systems in Campylobacterota (formerly Epsilonproteobacteria), a phylum with sufficient evolutionary depth and ecological diversity. We discovered that chemosensory system increases complexity by horizontal gene transfer (HGT) of entire chemosensory classes, and different chemosensory classes rarely mix their components. Two-component system gains complexity by atypical histidine kinases fused with receiver domain to achieve multistep or branched signal transduction process. The presence and complexity of c-di-GMP-mediated system is related to the size of signaling network, and c-di-GMP pathways are easy to rewire, since enzymes and effectors can be linked without direct protein-protein interaction. Overall, signaling capacity and complexity rise and drop together in Campylobacterota, determined by sensory demand, genetic resources, and coevolution within the genomic context. These findings reflect plausible evolutionary principles for other cellular networks and genome evolution of the Bacteria domain. IMPORTANCE Bacteria are capable of sensing and responding to environmental changes by several signal transduction systems with different mechanisms. Much attention is paid to model organisms with complex signaling networks to understand their composition and function, but how a complicated network evolved from a simple one or vice versa lacks systematic studies. Here, we tracked the evolutionary process of each signaling system in a bacterial phylum with robust "eco-evo" framework and summarized the general principles of signaling network evolution. Our findings bridge the gaps in bacterial signaling capacity from highly sophisticated to extremely streamlined, shedding light on rational design of genetic circuitry. This study may serve as a paradigm to examine the complex construction of other cellular networks and genome evolution.

Identification of Molecular Markers That Are Specific to the Class Thermoleophilia.

The class Thermoleophilia is one of the deep-rooting lineages within the Actinobacteria phylum and metagenomic investigation of microbial diversity suggested that species associated with the class Thermoleophilia are abundant in hot spring and soil samples. However, very few species of this class have been cultivated and characterized. Our understanding of the phylogeny and taxonomy of Thermoleophilia is solely based on 16S rRNA sequence analysis of limited cultivable representatives, but no other phenotypic or genotypic characteristics are known that can clearly discriminate members of this class from the other taxonomic units within the kingdom bacteria. This study reports phylogenomic analysis for 12 sequenced members of this class and clearly resolves the interrelationship of not yet cultivated species with reconstructed genomes and known type species. Comparative genome analysis discovered 12 CSIs in different proteins and 32 CSPs that are specific to all species of this class. In addition, a large number of CSIs or CSPs were identified to be unique to certain lineages within this class. This study represents the first and most comprehensive phylogenetic analysis of the class Thermoleophilia, and the identified CSIs and CSPs provide valuable molecular markers for the identification and delineation of species belonging to this class or its subordinate taxa.