Reinvestigating the phylogeny of Myriapoda with more extensive taxon sampling and novel genetic perspective

Background There have been extensive debates on the interrelationships among the four major classes of Myriapoda—Chilopoda, Symphyla, Diplopoda, and Pauropoda. The core controversy is the position of Pauropoda; that is, whether it should be grouped with Symphyla or Diplopoda as a sister group. Two recent phylogenomic studies separately investigated transcriptomic data from 14 and 29 Myriapoda species covering all four groups along with outgroups, and proposed two different topologies of phylogenetic relationships. Methods Building on these studies, we extended the taxon sampling by investigating 39 myriapods and integrating the previously available data with three new transcriptomic datasets generated in this study. Our analyses present the phylogenetic relationships among the four major classes of Myriapoda with a more abundant taxon sampling and provide a new perspective to investigate the above-mentioned question, where visual genes’ identification were conducted. We compared the appearance pattern of genes, grouping them according to their classes and the visual pathways involved. Positive selection was detected for all identified visual genes between every pair of 39 myriapods, and 14 genes showed positive selection among 27 pairs. Results From the results of phylogenomic analyses, we propose that Symphyla is a sister group of Pauropoda. This stance has also received strong support from tree inference and topology tests.

Chloroplast Phylogenomic Analyses Reveal a Maternal Hybridization Event Leading to the Formation of Cultivated Peanuts

Peanuts (Arachis hypogaea L.) offer numerous healthy benefits, and the production of peanuts has a prominent role in global food security. As a result, it is in the interest of society to improve the productivity and quality of peanuts with transgenic means. However, the lack of a robust phylogeny of cultivated and wild peanut species has limited the utilization of genetic resources in peanut molecular breeding. In this study, a total of 33 complete peanut plastomes were sequenced, analyzed and used for phylogenetic analyses. Our results suggest that sect. Arachis can be subdivided into two lineages. All the cultivated species are contained in Lineage I with AABB and AA are the two predominant genome types present, while species in Lineage II possess diverse genome types, including BB, KK, GG, etc. Phylogenetic studies also indicate that all allotetraploid cultivated peanut species have been derived from a possible maternal hybridization event with one of the diploid Arachis duranensis accessions being a potential AA sub-genome ancestor. In addition, Arachis monticola, a tetraploid wild species, is placed in the same group with all the cultivated peanuts, and it may represent a transitional species, which has been through the recent hybridization event. This research could facilitate a better understanding of the taxonomic status of various Arachis species/accessions and the evolutionary relationship among them, and assists in the correct and efficient use of germplasm resources in breeding efforts to improve peanuts for the benefit of human beings.

A target capture approach for phylogenomic analyses at multiple evolutionary timescales in rosewoods (Dalbergia spp.) and the legume family (Fabaceae)

Understanding the genetic changes associated with the evolution of biological diversity is of fundamental interest to molecular ecologists. The assessment of genetic variation at hundreds or thousands of unlinked genetic loci forms a sound basis to address questions ranging from micro- to macro-evolutionary timescales, and is now possible thanks to advances in sequencing technology. Major difficulties are associated with i) the lack of genomic resources for many taxa, especially from tropical biodiversity hotspots, ii) scaling the numbers of individuals analyzed and loci sequenced, and iii) building tools for reproducible bioinformatic analyses of such datasets. To address these challenges, we developed a set of target capture probes for phylogenomic studies of the highly diverse, pantropically distributed and economically significant rosewoods (Dalbergia spp.), explored the performance of an overlapping probe set for target capture across the legume family (Fabaceae), and built a general-purpose bioinformatics pipeline. Phylogenomic analyses of Dalbergia species from Madagascar yielded highly resolved and well supported hypotheses of evolutionary relationships. Population genomic analyses identified differences between closely related species and revealed the existence of a potentially new species, suggesting that the diversity of Malagasy Dalbergia species has been underestimated. Analyses at the family level corroborated previous findings by the recovery of monophyletic subfamilies and many well-known clades, as well as high levels of gene tree discordance, especially near the root of the family. The new genomic and bioinformatics resources will hopefully advance systematics and ecological genetics research in legumes, and promote conservation of the highly diverse and endangered Dalbergia rosewoods.

Phylogenomics unravels the early diversification of fungi

Our understanding of the eukaryote tree of life is continually improving, although the branching events at some of the deepest nodes remain elusive. The fungi are an ancient group of eukaryotes with a wide range of morphologies, life-history strategies, and ecological roles. While several recent phylogenomic analyses have been shown to be a powerful tool for uncovering even earliest diversifications, no study has yet examined the entire tree of fungi using a taxonomically comprehensive data set and suitable models of evolution. Here, we assembled a data set of 299 proteins from all recognised fungal groups for which genomic/transcriptomic data were available and subjected this to a battery of analyses, including tree inferences using site-heterogeneous mixture models and the Multi-Species Coalescent model. Tree topology was highly congruent and well supported, and any incongruence was found to result from an inability of some frequently used evolutionary models to model fast-evolving and heterogeneous sites. Our results provide higher resolution among early-branching lineages than previous studies, and shed light on hitherto highly contested evolutionary origins of the major fungal groups.

Phylogenomic analyses of Snodgrassella isolates from honeybees and bumblebees reveals taxonomic and functional diversity

Snodgrassella is a Betaproteobacteria genus found in the gut of honeybees (Apis spp.) and bumblebees (Bombus spp). It is part of a conserved microbiome that is composed of few core phylotypes and is essential for bee health and metabolism. Phylogenomic analyses using whole genome sequences of 75 Snodgrassella strains from 4 species of honey bees and 14 species of bumblebees showed that these strains formed a monophyletic lineage within the Neisseriaceae family, that Snodgrassella isolates from Asian honeybees diverged early on from the other species in their evolution, that isolates from honeybees and bumblebees were well separated and that this genus consists of at least seven species. We propose to formally name two new Snodgrassella species that were isolated from bumblebees, i.e. Snodgrassella gandavensis sp. nov. and Snodgrassella communis sp. nov. Possible evolutionary scenarios for 107 species or group specific genes revealed very limited evidence for horizontal gene transfer. Functional analyses revealed the importance of small proteins, defense mechanisms, amino acid transport and metabolism, inorganic ion transport and metabolism and carbohydrate transport and metabolism among these 107 specific genes.ImportanceThe microbiome of honeybees (Apis spp.) and bumblebees (Bombus spp.) is highly conserved and represented by few phylotypes. This simplicity in taxon composition makes the bee’s microbiome an emergent model organism for the study of gut microbial communities. Since the description of the Snodgrassella genus, which was isolated from the gut of honeybees and bumblebees in 2013, a single species, i.e. Snodgrassella alvi, has been named. Here we demonstrate that this genus is actually composed of at least seven species, two of them (Snodgrassella gandavensis sp. nov. and Snodgrassella communis sp. nov.) being formally described in the present publication. We also report the presence of 107 genes specific to Snodgrassella species, showing notably the importance of small proteins and defense mechanisms in this genus.Data summaryCornet L and Vandamme P, European Nucleotide Archive (ENA), Project accession: PRJEB47378Cornet L and Vandamme P, European Nucleotide Archive (ENA), Reads accessions: SAMEA9570070 - SAMEA9570078Cornet L and Vandamme P, European Nucleotide Archive (ENA), Genome accessions: GCA_914768015, GCA_914768025, GCA_914768035, GCA_914768045, GCA_914768055, GCA_914768065, GCA_914768075, GCA_914768085, GCA_914768095.

Taxonomic updates to Artocarpus subgenus Artocarpus (Moraceae) and allied taxa with a particular focus on the species native to Singapore

The breadfruit genus Artocarpus J.R.Forst. & G.Forst. (Moraceae) has sixteen species in Singapore, fourteen of them native. In this precursory study to the treatment of Artocarpus for the Flora of Singapore, we present updated phylogenomic analyses of Artocarpus subgenus Artocarpus based on 517 nuclear genes. The following taxonomic changes based on recent phylogenetic analyses, review of herbarium specimens, and field observations, are proposed. Artocarpus subg. Cauliflori (F.M.Jarrett) Zerega is reduced to a section within Artocarpus subg. Artocarpus, and Artocarpus sect. Glandulifolium F.M.Jarrett is raised to subgenus status. The new monotypic subgenus Artocarpus subg. Aenigma E.M.Gardner & Zerega is proposed for Artocarpus sepicanus Diels, whose phylogenetic position remains uncertain and may be of ancient hybrid origin. Artocarpus elasticus Reinw. ex Blume, A. scortechinii King and A. corneri Kochummen are recognised as distinct species. Artocarpus clementis Merr. is reinstated as distinct from A. lanceifolius Roxb. Artocarpus calophyllus Kurz and A. melinoxylus Gagnep. are reinstated as distinct from both A. chama Buch.-Ham. and A. rigidus Blume. Artocarpus nigrescens Elmer is reinstated as distinct from A. treculianus Elmer. Keys to the subgenera, the sections of Artocarpus subg. Artocarpus and to the species found in Singapore are presented. A nomenclatural synopsis of subgenera Artocarpus, Aenigma and Glandulifolium is presented with taxonomic notes to aid in identification. Seventeen lectotypes, six of them in a second step, and two neotypes are designated.

Comparative and phylogenomic analyses of mitochondrial genomes in Coccinellidae (Coleoptera: Coccinelloidea)

The Coccinellidae are one of the most familiar beetle families, the ladybirds. Despite the great ecological and economic significance, the phylogenetic relationships of Coccinellidae remain poorly understood. One of the reasons is that the sequenced mitogenomes available for this family are very limited. We sequenced complete or nearly complete mitogenomes from seven species of the tribe Coccinellini with next-generation sequencing. All species have the same gene content and gene order as the putatively ancestral insect mitogenome. A large intergenic spacer region (> 890 bp) was found located between trnI and trnQ. The potential for using secondary structures of the large and small ribosomal subunits for phylogenetic reconstruction was predicted. The phylogenetic relationships were explored through comparative analyses across more than 30 coccinellid species. We performed phylogenetic analyses with both concatenation methods (Maximum Likelihood and Bayesian Inference) and multispecies coalescent method (ASTRAL). Phylogenetic results strongly supported the monophyly of Coccinellidae. Within Coccinellidae, the Epilachnini and the Coccinellini including Halyziini were monophyletic, while the Scymnini and Coccidulini were non-monophyletic.

A target capture approach for phylogenomic analyses at multiple evolutionary timescales in rosewoods (Dalbergia spp.) and the legume family (Fabaceae)

Understanding the genetic changes associated with the evolution of biological diversity is of fundamental interest to molecular ecologists. The assessment of genetic variation at hundreds or thousands of unlinked genetic loci forms a sound basis to address questions ranging from micro- to macro-evolutionary timescales, and is now possible thanks to advances in sequencing technology. Major difficulties are associated with i) the lack of genomic resources for many taxa, especially from tropical biodiversity hotspots, ii) scaling the numbers of individuals analyzed and loci sequenced, and iii) building tools for reproducible bioinformatic analyses of such datasets. To address these challenges, we developed a set of target capture probes for phylogenomic studies of the highly diverse, pantropically distributed and economically significant rosewoods (Dalbergia spp.), explored the performance of an overlapping probe set for target capture across the legume family (Fabaceae), and built a general-purpose bioinformatics pipeline. Phylogenomic analyses of Dalbergia species from Madagascar yielded highly resolved and well supported hypotheses of evolutionary relationships. Population genomic analyses identified differences between closely related species and revealed the existence of a potentially new species, suggesting that the diversity of Malagasy Dalbergia species has been underestimated. Analyses at the family level corroborated previous findings by the recovery of monophyletic subfamilies and many well-known clades, as well as high levels of gene tree discordance, especially near the root of the family. The new genomic and bioinformatics resources will hopefully advance systematics and ecological genetics research in legumes, and promote conservation of the highly diverse and endangered Dalbergia rosewoods.