Phylogenomic and comparative analyses on protein sequences from Halobacteria to identify taxon-specific molecular markers which demarcate different Halobacteriaceae and Haloarculaceae genera
Bibliographic record
Abstract
Members of the class Halobacteria , due to their widespread distribution in different high-salt environments and potential biotechnological applications, are being discovered at a rapid pace. In recent years, the classification of Halobacteria has undergone major changes, and this class is now divided into 10 families consisting of >77 genera. However, different Halobacteria taxa are presently distinguished based mainly on their branching in phylogenomic trees. No specific characteristics are known which are unique to members of different taxa. To advance our understanding of Halobacteria taxa in this regard, we report here comprehensive phylogenomic and comparative analyses on species from two Halobacteria families, viz. Haloarculaceae and Halobacteriaceae . A phylogenomic tree for 385 Halobacteria species constructed in this work supported the current taxonomy. However, the main objective of this study was to identify molecular markers consisting of conserved signature indels (CSIs) in protein sequences which are uniquely found in the species from the above two families, or those which are specific to their different genera. Our work has identified 105 CSIs in diverse proteins, some of which are specific to Halobacteriaceae , whereas others are exclusively shared characteristics of different Haloarculaceae and Halobacteriaceae genera. Based upon the described CSIs, all genera from these two families containing two or more named species (viz. Halapricum , Halarchaeum , Haloarcula , Halobacterium , Halocatena , Haloglomus , Halomarina , Halomicrobium , Halorarius , Halorhabdus , Halorientalis , Halosegnis , Halosimplex , Halovenus and Natronomonas ) can be robustly distinguished from all other Halobacteria genera. The identified CSIs, which are also present in uncharacterized strains of these taxa, provide more definitive means for the demarcation of these Halobacteria taxa and for the identification of new species/strains related to these genera. Because of the predicted functional importance of these CSIs, these taxon-specific molecular markers also provide novel tools for genetic, biochemical and functional studies on these groups of Halobacteria .
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".