PhyloHerb: A high-throughput phylogenomic pipeline for processing genome skimming data

Phylogenomics of endemic Australian Ulopinae (Hemiptera: Cicadomorpha: Cicadellidae)

Ulopinae is a distinctive subfamily of leafhoppers that is widely distributed across the Afrotropical, Palearctic, Indomalayan and Australasian regions. The ulopine fauna of Australia is entirely endemic and includes two tribes of striking appearance, the Ulopini and Cephalelini. Knowledge of these groups is fragmentary and in many instances, no information is available beyond original descriptions. We assess the monophyly, phylogenetic placement and species-level diversity of the Ulopini genus Austrolopa . Phylogenetic analyses based on sequence data from target nuclear loci (18S , 28S , H2A and H3 ) and mitochondrial genomes (15 genes) for 23 membracoid taxa yielded congruent topologies. Our results provide strong evidence for the monophyly of Ulopinae and a clade consisting of Ulopini + Cephalelini. However, a non-monophyletic Cephalelini arises from within a polyphyletic Ulopini. Austrolopa was strongly recovered as monophyletic in all analyses, a result also supported by morphological features. The genus currently includes six species, three of which are described based on morphological and molecular data: Austrolopa botanica , sp. nov. , Austrolopa rotunda , sp. nov. and Austrolopa sublima , sp. nov. A lectotype designation is provided for Austrolopa kingensis Evans, 1937, sp. reval. Our findings illustrate that the Australian Ulopinae is far more diverse than currently circumscribed and several species of Austrolopa are yet to be recognised. ZooBank: urn:lsid:zoobank.org:pub:1480285B-8F61-4659-A929-2B1EF3168868.

Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates

Genome skimming is defined as low-pass sequencing below 0.05× coverage and is typically used for mitochondrial genome recovery and species identification. Long-read nanopore sequencers enable simultaneous reading of both DNA sequence and methylation and can multiplex samples for low-cost genome skimming. Here I present nanopore sequencing as a highly precise platform for global DNA methylation and transposon assessment. At coverage of just 0.001×, or 30 Mb of reads, accuracy is sub-1%. Biological and technical replicates validate high precision. Skimming 40 vertebrate species reveals conserved patterns of global methylation consistent with whole-genome bisulfite sequencing and an average mapping rate >97%. Genome size directly correlates to global DNA methylation, explaining 39% of its variance. Accurate SINE and LINE transposon methylation in both the mouse and primates can be obtained with just 0.0001× coverage, or 3 Mb of reads. Sample multiplexing, field portability, and the low price of this instrument combine to make genome skimming for DNA methylation an accessible method for epigenetic assessment from ecology to epidemiology and for low-resource groups.

Characterizing conflict and congruence of molecular evolution across organellar genome sequences for phylogenetics in land plants

Chloroplasts and mitochondria each contain their own genomes, which have historically been and continue to be important sources of information for inferring the phylogenetic relationships among land plants. The organelles are predominantly inherited from the same parent, and therefore should exhibit phylogenetic concordance. In this study, we examine the mitochondrion and chloroplast genomes of 226 land plants to infer the degree of similarity between the organelles' evolutionary histories. Our results show largely concordant topologies are inferred between the organelles, aside from four well-supported conflicting relationships that warrant further investigation. Despite broad patterns of topological concordance, our findings suggest that the chloroplast and mitochondrial genomes evolved with significant differences in molecular evolution. The differences result in the genes from the chloroplast and the mitochondrion preferentially clustering with other genes from their respective organelles by a program that automates selection of evolutionary model partitions for sequence alignments. Further investigation showed that changes in compositional heterogeneity are not always uniform across divergences in the land plant tree of life. These results indicate that although the chloroplast and mitochondrial genomes have coexisted for over 1 billion years, phylogenetically, they are still evolving sufficiently independently to warrant separate models of evolution. As genome sequencing becomes more accessible, research into these organelles' evolution will continue revealing insight into the ancient cellular events that shaped not only their history, but the history of plants as a whole.

Phylogenomics and taxon-rich phylogenies of new and historical specimens shed light on the systematics of Hypnea (Cystocloniaceae, Rhodophyta)

Cystocloniacae is a highly diverse family of Rhodophyta, including species of ecological and economic importance, whose phylogeny remains largely unresolved. Species delimitation is unclear, particularly in the most speciose genus, Hypnea, and cryptic diversity has been revealed by recent molecular assessments, especially in the tropics. Here, we carried out the first phylogenomic investigation of Cystocloniaceae, focused on the genus Hypnea, inferred from chloroplast and mitochondrial genomes including taxa sampled from new and historical collections. In this work, molecular synapomorphies (gene losses, InDels and gene inversions) were identified to better characterize clades in our congruent organellar phylogenies. We also present taxon-rich phylogenies based on plastid and mitochondrial markers. Molecular and morphological comparisons of historic collections with contemporary specimens revealed the need for taxonomic updates in Hypnea, the synonymization of H. marchantae to a later heterotypic synonym of H. cervicornis and the description of three new species: H. davisiana sp. nov., H. djamilae sp. nov. and H. evaristoae sp. nov.

The herbarium of the future

The ~400 million specimens deposited across ~3000 herbaria are essential for: (i) understanding where plants have lived in the past, (ii) forecasting where they may live in the future, and (iii) delineating their conservation status. An open access 'global metaherbarium' is emerging as these specimens are digitized, mobilized, and interlinked online. This virtual biodiversity resource is attracting new users who are accelerating traditional applications of herbaria and generating basic and applied scientific innovations, including e-monographs and floras produced by diverse, interdisciplinary, and inclusive teams; robust machine-learning algorithms for species identification and phenotyping; collection and synthesis of ecological trait data at large spatiotemporal and phylogenetic scales; and exhibitions and installations that convey the beauty of plants and the value of herbaria in addressing broader societal issues.

A pipeline for assembling low copy nuclear markers from plant genome skimming data for phylogenetic use

Background

Genome skimming is a popular method in plant phylogenomics that do not include a biased enrichment step, relying on random shallow sequencing of total genomic DNA. From these data the plastome is usually readily assembled and constitutes the bulk of phylogenetic information generated in these studies. Despite a few attempts to use genome skims to recover low copy nuclear loci for direct phylogenetic use, such endeavor remains neglected. Causes might include the trade-off between libraries with few reads and species with large genomes (i.e., missing data caused by low coverage), but also might relate to the lack of pipelines for data assembling.

Methods

A pipeline and its companion R package designed to automate the recovery of low copy nuclear markers from genome skimming libraries are presented. Additionally, a series of analyses aiming to evaluate the impact of key assembling parameters, reference selection and missing data are presented.

Results

A substantial amount of putative low copy nuclear loci was assembled and proved useful to base phylogenetic inference across the libraries tested (4 to 11 times more data than previously assembled plastomes from the same libraries).

Discussion

Critical aspects of assembling low copy nuclear markers from genome skims include the minimum coverage and depth of a sequence to be used. More stringent values of these parameters reduces the amount of assembled data and increases the relative amount of missing data, which can compromise phylogenetic inference, in turn relaxing the same parameters might increase sequence error. These issues are discussed in the text, and parameter tuning through multiple comparisons tracking their effects on support and congruence is highly recommended when using this pipeline. The skimmingLoci pipeline (https://github.com/mreginato/skimmingLoci) might stimulate the use of genome skims to recover nuclear loci for direct phylogenetic use, increasing the power of genome skimming data to resolve phylogenetic relationships, while reducing the amount of sequenced DNA that is commonly wasted.