MT-MAG: Accurate and interpretable machine learning based taxonomic assignment of metagenome-assembled genomes, with a partial classification option

We propose MT-MAG, a novel machine learning-based taxonomic assignment tool for hierarchically-structured local classification of metagenome-assembled genomes (MAGs). MT-MAG is capable of classifying large and diverse real metagenomic datasets, having analyzed for this study a total of 240 Gbp of data in the training set, and 7 Gbp of data in the test set. MT-MAG is, to the best of our knowledge, the first machine learning method for taxonomic assignment of metagenomic data that offers a "partial classification" option. MT-MAG outputs complete or a partial classification paths, and interpretable numerical classification confidences of its classifications, at all taxonomic ranks. MT-MAG is able to completely classify 48% more sequences than DeepMicrobes to the Species level (the only comparable taxonomic rank for DeepMicrobes), and it outperforms DeepMicrobes by an average of 33% in weighted accuracy, and by 89% in constrained accuracy.

A divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the Archaea

Background The recent rise in cultivation-independent genome sequencing has provided key material to explore uncharted branches of the Tree of Life. This has been particularly spectacular concerning the Archaea, projecting them at the center stage as prominently relevant to understand early stages in evolution and the emergence of fundamental metabolisms as well as the origin of eukaryotes. Yet, resolving deep divergences remains a challenging task due to well-known tree-reconstruction artefacts and biases in extracting robust ancient phylogenetic signal, notably when analyzing data sets including the three Domains of Life. Among the various strategies aimed at mitigating these problems, divide-and-conquer approaches remain poorly explored, and have been primarily based on reconciliation among single gene trees which however notoriously lack ancient phylogenetic signal. Results We analyzed sub-sets of full supermatrices covering the whole Tree of Life with specific taxonomic sampling to robustly resolve different parts of the archaeal phylogeny in light of their current diversity. Our results strongly support the existence and early emergence of two main clades, Cluster I and Cluster II, which we name Ouranosarchaea and Gaiarchaea, and we clarify the placement of important novel archaeal lineages within these two clades. However, the monophyly and branching of the fast evolving nanosized DPANN members remains unclear and worth of further study. Conclusions We inferred a well resolved rooted phylogeny of the Archaea that includes all recently described phyla of high taxonomic rank. This phylogeny represents a valuable reference to study the evolutionary events associated to the early steps of the diversification of the archaeal domain. Beyond the specifics of archaeal phylogeny, our results demonstrate the power of divide-and-conquer approaches to resolve deep phylogenetic relationships, which should be applied to progressively resolve the entire Tree of Life.

Protein Complex Structure Prediction Powered by Multiple Sequence Alignment of Interologs from Multiple Taxonomic Ranks and AlphaFold2

AlphaFold2 is expected to be able to predict protein complex structures as long as a multiple sequence alignment (MSA) of the interologs of the target protein-protein interaction (PPI) can be provided. However, preparing the MSA of protein-protein interologs is a non-trivial task. In this study, a simplified phylogeny-based approach was applied to generate the MSA of interologs, which was then used as the input of AlphaFold2 for protein complex structure prediction. Extensively benchmarked this protocol on non-redundant PPI dataset, we show complex structures of 79.5% of the bacterial PPIs and 49.8% of the eukaryotic PPIs can be successfully predicted. Considering PPIs may not be conserved in species with long evolutionary distances, we further restricted interologs in the MSA to different taxonomic ranks of the species of the target PPI in protein complex structure prediction. We found the success rates can be increased to 87.9% for the bacterial PPIs and 56.3% of the eukaryotic PPIs if interologs in the MSA are restricted to a specific taxonomic rank of the species of each target PPI. Finally, we show the optimal taxonomic ranks for protein complex structure prediction can be selected with the application of the predicted TM-scores of the output models.

The effect of soil sample size, for practical DNA extraction, on soil microbial diversity in different taxonomic ranks

To determine the optimal soil sample size for microbial community structure analysis, DNA extraction, microbial composition analysis, and diversity assessments were performed using soil sample sizes of 0.2, 1, and 5 g. This study focused on the relationship between soil amount and DNA extraction container volume and the alteration in microbial composition at different taxonomic ranks (order, class, and phylum). Horizontal (0.2 and 1 g) and vertical (5 g) shaking were applied during DNA extraction for practical use in a small laboratory. In the case of the 5 g soil sample, DNA extraction efficiency and the value of α-diversity index fluctuated severely, possibly because of vertical shaking. Regarding the 0.2 and 1 g soil samples, the number of taxa, Shannon–Wiener index, and Bray–Curtis dissimilarity were stable and had approximately the same values at each taxonomic rank. However, non-metric multidimensional scaling showed that the microbial compositions of these two sample sizes were different. The higher relative abundance of taxa in the case of the 0.2 g soil sample might indicate that cell wall compositions differentiated the microbial community structures in these two sample sizes due to high shear stress tolerance. The soil sample size and tube volume affected the estimated microbial community structure. A soil sample size of 0.2 g would be preferable to the other sample sizes because of the possible higher shearing force for DNA extraction and lower experimental costs due to smaller amounts of consumables. When the taxonomic rank was changed from order to phylum, some minor taxa identified at the order rank were integrated into major taxa at the phylum rank. The integration affected the value of the β-diversity index; therefore, the microbial community structure analysis, reproducibility of structures, diversity assessment, and detection of minor taxa would be influenced by the taxonomic rank applied.

Complete Mitogenome of Endangered and Endemic Nicobar Treeshrew (Tupaia Nicobarica) and Comparison with Other Scandentians

The Nicobar treeshrew (Tupaia nicobarica) is an endangered smaller mammal endemic to the Nicobar Island of the Andaman Sea, India regarded as an alternative experimental animal model in biomedical research. The present study aimed to assemble the first mitochondrial genome of T. nicobarica to elucidate evolutionary relationship. The structure and variation of the novel mitochondrial genome were analyzed and compared with other Scandentians. The complete mitogenome (17,164 bp) encodes 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA (rRNAs), and one control region (CR). Most of the genes were encoded on majority strand, except nad6 and eight tRNAs. The nonsynonymous/synonymous ratio in all PCGs indicates strong negative selection among all Tupaiidae species. The comparative study of CRs revealed the occurrence of tandem repeats (CGTACA) found in T. nicobarica. The phylogenetic analyses (ML and BA) showed distinct clustering of T. nicobarica with high branch supports and depict a substantial divergence time (11.4 to 18.8 MYR) from the ancestor lineage of Tupaiidae. The 16S rRNA dataset corroborates the taxonomic rank of two subspecies of T. nicobarica from the Great and Little Nicobar Islands. The present study suggests the assembly of whole-genome to improve the understanding of evolutionary relationships of treeshrews and its implication in biomedical research.

Holotypes for three Caspian gastropods of the family Hydrobiidae tracked down: description and taxonomic interpretations

Type series of three nominal taxa of the hydrobiid gastropods inhabiting the Caspian Sea were traced recently in the uncatalogued part of the malacological collection of the Zoological Institute of Russian Academy of Sciences, Saint-Petersburg. Images of the holotypes and some paratypes of Pyrgula isseli Logvinenko & Starobogatov, 1969, P. sowinskyi Logvinenko & Starobogatov, 1969 and P. derzhavini Logvinenko & Starobogatov, 1969 are presented. The first two species belong to the genus Clathrocaspia (subfamily Caspiinae) and P. sowinskyi is considered a junior synonym of C. pallasii (Clessin & W. Dybowski in W. Dybowski, 1887). The attribution of the third species, P. derzhavini, to Laevicaspia (Pyrgulinae) is confirmed based on the newly discovered type material. Based on the additional information we update ecological data and distribution ranges of the species, provide comments on their nomenclature, systematic position and taxonomic rank.

A demographic and ecological study of an Italian population of Polyommatus ripartii: the ESU Polyommatus exuberans

Polyommatus exuberans is an evolutionarily significant unit (ESU) of the lycaenid butterfly Polyommatus ripartii. This ESU is known to survive at only two sites in the Susa Valley (NW Italy). Lack of correct management, reforestation and frequent wildfires severely threaten this ESU (listed as endangered species in the most recent IUCN Italian Red List). Although the taxonomic rank of this taxon is still debated, current threats could cause extinction of its two remaining populations before its taxonomic rank and its ecology are clarified. We collected data for the first time on this population at the small site of Mompantero (ab. 10 ha). We used butterfly GPS-positioning and the mark-release-recapture (MRR)-method to estimate its population size (269 individuals), sex-ratio (1.36 M/F), lifespan (4.76 days), density (47/ha) and mobility (median 153 and 33 m for males and females, respectively). Both sexes are equally catchable. Catchability increases around midday and decreases during overcast weather. While the size and density of this small population are comparable to those of other endemic Polyommatus species (such as P. humedasae and P. gennargenti), scarce mobility makes its populations isolated and even more seriously threatened. Implications for insect conservation We suggest that implementing an active management plan, including mowing before July and/or in autumn, and supporting ant diversity, is of immediate importance. Management should be extended to road verges, where the larval host plant (Onobrychis sp.) is abundant, and would thus also serve as corridors to favour dispersion between sites. Our research is the first study to investigate this taxon, thus shedding some light on the ecological and biological aspects that are crucial for long-term survival.

A global survey of specialized metabolic diversity encoded in bacterial genomes

Bacterial secondary metabolites have been studied for decades for their usefulness as drugs, such as antibiotics. However, the identification of new structures has been decelerating, in part due to rediscovery of known compounds. Meanwhile, multi-resistant pathogens continue to emerge, urging the need for new antibiotics. It is unclear how much chemical diversity exists in Nature and whether discovery efforts should be focused on established antibiotic producers or rather on understudied taxa. Here, we surveyed around 170,000 bacterial genomes as well as several thousands of Metagenome Assembled Genomes (MAGs) for their diversity in Biosynthetic Gene Clusters (BGCs) known to encode the biosynthetic machinery for producing secondary metabolites. We used two distinct algorithms to provide a global overview of the biosynthetic diversity present in the sequenced part of the bacterial kingdom. Our results indicate that only 3% of genomic potential for natural products has been experimentally discovered. We connect the emergence of most biosynthetic diversity in evolutionary history close to the taxonomic rank of genus. Despite enormous differences in potential among taxa, we identify Streptomyces as by far the most biosynthetically diverse based on currently available data. Simultaneously, our analysis highlights multiple promising high-producing taxas that have thus far escaped investigation.

A change in the taxonomic rank of Senna andhrica P. V. Ramana, J. Swamy & M. Ahmed. (Fabaceae: Caesalpinioideae)

Senna andhrica P. V. Ramana, J. Swamy & M. Ahmed. is better treated as a variety of S. occidentalis (L.) Link, as S. occidentalis var. andhrica (P. V. Ramana, J. Swamy & M. Ahmedullah) K. W. Jiang, based on its diagnostic morphological characters of unifoliolate leaves and 2–3 carpellate gynoecium. Attention is drawn to an error in the original figure published with the description of Senna andhirica, the seeds specified by the authors are actually belong to a taxon of Crotalaria.