Bathymetric evolution of black corals through deep time.

Deep-sea lineages are generally thought to arise from shallow-water ancestors, but this hypothesis is based on a relatively small number of taxonomic groups. Anthozoans, which include corals and sea anemones, are significant contributors to the faunal diversity of the deep sea, but the timing and mechanisms of their invasion into this biome remain elusive. Here, we reconstruct a fully resolved, time-calibrated phylogeny of 83 species in the order Antipatharia (black coral) to investigate their bathymetric evolutionary history. Our reconstruction indicates that extant black coral lineages first diversified in continental slope depths (∼250-3000 m) during the early Silurian (∼437 millions of years ago (Ma)) and subsequently radiated into, and diversified within, both continental shelf (less than 250 m) and abyssal (greater than 3000 m) habitats. Ancestral state reconstruction analysis suggests that the appearance of morphological features that enhanced the ability of black corals to acquire nutrients coincided with their invasion of novel depths. Our findings have important conservation implications for anthozoan lineages, as the loss of 'source' slope lineages could threaten millions of years of evolutionary history and confound future invasion events, thereby warranting protection.

Seabed mining could come at a high price for a unique fauna.

The deep seafloor is teeming with life, most of which remains poorly known to science. It also constitutes an important reserve of natural resources, particularly minerals, that mining companies will start harvesting in the next few years (Nat Rev Earth Environ, 1, 2020, 158). In this context, broad biodiversity assessments of deep-sea ecosystems are urgently needed to establish a baseline prior to mining. However, significant gaps in our taxonomic knowledge and the high cost of sampling in the deep sea limit the effectiveness of conventional morphology-based surveys. In this issue of Molecular Ecology, Laroche et al. (Mol Ecol, 2020) capitalize on high throughput molecular methods to conduct one of the most detailed and rigorous surveys of the composition and biogeography of deep-seafloor metazoan communities to date. The authors show that deep seamounts in the Clarion Clipperton Zone are inhabited by rich metazoan communities that are distinct from those of the surrounding abyssal plains. These results have important conservation implications: if communities on deep seamounts were to persist after large-scale industrial mining operations on the surrounding plains, the seamounts would not serve as appropriate reservoirs to repopulate impacted areas.

Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes.

BACKGROUND: Alternative polyadenylation (APA) results in messenger RNA molecules with different 3' untranslated regions (3' UTRs), affecting the molecules' stability, localization, and translation. APA is pervasive and implicated in cancer. Earlier reports on APA focused on 3' UTR length modifications and commonly characterized APA events as 3' UTR shortening or lengthening. However, such characterization oversimplifies the processing of 3' ends of transcripts and fails to adequately describe the various scenarios we observe. RESULTS: We built a cloud-based targeted de novo transcript assembly and analysis pipeline that incorporates our previously developed cleavage site prediction tool, KLEAT. We applied this pipeline to elucidate the APA profiles of 114 genes in 9939 tumor and 729 tissue normal samples from The Cancer Genome Atlas (TCGA). The full set of 10,668 RNA-Seq samples from 33 cancer types has not been utilized by previous APA studies. By comparing the frequencies of predicted cleavage sites between normal and tumor sample groups, we identified 77 events (i.e. gene-cancer type pairs) of tumor-specific APA regulation in 13 cancer types; for 15 genes, such regulation is recurrent across multiple cancers. Our results also support a previous report showing the 3' UTR shortening of FGF2 in multiple cancers. However, over half of the events we identified display complex changes to 3' UTR length that resist simple classification like shortening or lengthening. CONCLUSIONS: Recurrent tumor-specific regulation of APA is widespread in cancer. However, the regulation pattern that we observed in TCGA RNA-seq data cannot be described as straightforward 3' UTR shortening or lengthening. Continued investigation into this complex, nuanced regulatory landscape will provide further insight into its role in tumor formation and development.

Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism.

White spruce (Picea glauca), a gymnosperm tree, has been established as one of the models for conifer genomics. We describe the draft genome assemblies of two white spruce genotypes, PG29 and WS77111, innovative tools for the assembly of very large genomes, and the conifer genomics resources developed in this process. The two white spruce genotypes originate from distant geographic regions of western (PG29) and eastern (WS77111) North America, and represent elite trees in two Canadian tree-breeding programs. We present an update (V3 and V4) for a previously reported PG29 V2 draft genome assembly and introduce a second white spruce genome assembly for genotype WS77111. Assemblies of the PG29 and WS77111 genomes confirm the reconstructed white spruce genome size in the 20 Gbp range, and show broad synteny. Using the PG29 V3 assembly and additional white spruce genomics and transcriptomics resources, we performed MAKER-P annotation and meticulous expert annotation of very large gene families of conifer defense metabolism, the terpene synthases and cytochrome P450s. We also comprehensively annotated the white spruce mevalonate, methylerythritol phosphate and phenylpropanoid pathways. These analyses highlighted the large extent of gene and pseudogene duplications in a conifer genome, in particular for genes of secondary (i.e. specialized) metabolism, and the potential for gain and loss of function for defense and adaptation.

Lessons from assembling UCEs: A comparison of common methods and the case of Clavinomia (Halictidae).

Sequence data assembly is a foundational step in high-throughput sequencing, with untold consequences for downstream analyses. Despite this, few studies have interrogated the many methods for assembling phylogenomic UCE data for their comparative efficacy, or for how outputs may be impacted. We study this by comparing the most commonly used assembly methods for UCEs in the under-studied bee lineage Nomiinae and a representative sampling of relatives. Data for 63 UCE-only and 75 mixed taxa were assembled with five methods, including ABySS, HybPiper, SPAdes, Trinity and Velvet, and then benchmarked for their relative performance in terms of locus capture parameters and phylogenetic reconstruction. Unexpectedly, Trinity and Velvet trailed the other methods in terms of locus capture and DNA matrix density, whereas SPAdes performed favourably in most assessed metrics. In comparison with SPAdes, the guided-assembly approach HybPiper generally recovered the highest quality loci but in lower numbers. Based on our results, we formally move Clavinomia to Dieunomiini and render Epinomia once more a subgenus of Dieunomia. We strongly advise that future studies more closely examine the influence of assembly approach on their results, or, minimally, use better-performing assembly methods such as SPAdes or HybPiper. In this way, we can move forward with phylogenomic studies in a more standardized, comparable manner.

An insight into the prokaryotic diversity from a polymetallic nodule-rich region in the Central Indian Ocean Basin using next generation sequencing approach.

Deep sea is a vast, dark, and difficult-to-access terrain and is now looked upon as a unique niche harboring diverse microorganism. We used a metataxonomic approach to decipher the microbial diversity present in the water column (surface to near bottom), water overlaying the sediments, and the deep-sea sediments (up to 35 cm) from the Indian Contract Region (ICR) in the Central Indian Ocean Basin (CIOB). Samples were collected from #IRZ (Impact Reference Zone), #PRZ (Potential Reference Zone), and #BC20 (Control site, outside potential mining area) with an average water depth of 5,200 m. 16S rRNA (V3-V4 region) amplicon sequencing on the MiSeq platform resulted in 942,851 ASVs across 65 water and sediment samples. Higher prokaryotic diversity was observed below 200 m in the water column to the seafloor. Proteobacteria was the most dominant bacterial phylum among all the water samples while Firmicutes, Actinobacteria and, Bacteroidota dominated the sediments. Sediment (below 10 cm) was co-dominated by Firmicutes. Thermoplasmata was the dominant archaeal group in the water column while Crenarchaeota was in the sediments. BC20 was less diverse than IRZ and PRZ. Deep Sea microorganisms could play a vital role in the mineralization processes, nutrient cycling, and also different biogeochemical cycles.

Delayed response of hermit crabs carrying anemones to a benthic impact experiment at the deep-sea nodule fields of the Peru Basin?

The deep Peru Basin is characterised by a unique abyssal scavenging community featuring large numbers of hermit crabs (Probeebei mirabilis, Decapoda, Crustacea). These are atypical hermit crabs, not carrying a shell, but on some occasions carrying an anemone (Actiniaria). The reason why some hermit crabs carry or not carry anemones is thought to be indicative of a changed environment, outweighing the cost/benefit of their relationship. Here we present the temporal variation of abundances of P. mirabilis with and without anemones, spanning more than two decades, following a benthic impact experiment. An overall decrease in hermit crab densities was observed, most noticeable and significant after 26 years and characterised by a loss of Actiniaria on the Probeebei mirabilis' pleon. Whether this is a delayed response to the benthic impact experiment carried out 26 years' prior or a natural variation in the population remains to be corroborated by an extension of the time-series. Attention is drawn to the limitations of our knowledge over time and space of the abyssal community dynamics and the urgent necessity to fill in these gaps prior to any type of deep-sea exploitation.

An updated de novo transcriptome for green ash (Fraxinus pennsylvanica).

De novo transcriptome assembly of next-generation sequencing information has become a powerful tool for the study of non-model species. Transcriptomes generated by this method can have high variability due to endless combinations of user-defined variables and programs available for assembly. Many methods have been developed for evaluating the quality of these assemblies. Here, raw sequencing information for Green ash (Fraxinus pennsylvanica Marshall) that was previously published has been re-evaluated. An updated assembly has been developed by including additional sequencing information not used for the currently accepted transcriptome in combination with more stringent trimming parameters. Input reads were assembled with Trinity and Abyss assembly programs. The resulting Trinity assembly has a 7.3-fold increase in genomic breadth of coverage, a 2.4-fold increase in predicted complete open reading frames, an increased L50 value, and increased Benchmarking Universal Single-Copy Ortholog completeness compared to the earlier published transcriptome. This updated transcriptome can be leveraged to help fight the rapid decline of green ash due to pathogens.

How many metazoan species live in the world's largest mineral exploration region?

The global surge in demand for metals such as cobalt and nickel has created unprecedented interest in deep-sea habitats with mineral resources. The largest area of activity is a 6 million km2 region known as the Clarion-Clipperton Zone (CCZ) in the central and eastern Pacific, regulated by the International Seabed Authority (ISA). Baseline biodiversity knowledge of the region is crucial to effective management of environmental impact from potential deep-sea mining activities, but until recently this has been almost completely lacking. The rapid growth in taxonomic outputs and data availability for the region over the last decade has allowed us to conduct the first comprehensive synthesis of CCZ benthic metazoan biodiversity for all faunal size classes. Here we present the CCZ Checklist, a biodiversity inventory of benthic metazoa vital to future assessments of environmental impacts. An estimated 92% of species identified from the CCZ are new to science (436 named species from a total of 5,578 recorded). This is likely to be an overestimate owing to synonyms in the data but is supported by analysis of recent taxonomic studies suggesting that 88% of species sampled in the region are undescribed. Species richness estimators place total CCZ metazoan benthic diversity at 6,233 (+/-82 SE) species for Chao1, and 7,620 (+/-132 SE) species for Chao2, most likely representing lower bounds of diversity in the region. Although uncertainty in estimates is high, regional syntheses become increasingly possible as comparable datasets accumulate. These will be vital to understanding ecological processes and risks of biodiversity loss.

Impact of returning scientific cruises and prolonged on-site presence on litter abundance at the deep-sea nodule fields in the Peru Basin.

Marine litter can be found along coasts, continental shelves and slopes, down into the abyss. The absence of light, low temperatures and low energy regimes characterising the deeper habitats ensure the persistence of litter over time. Therefore, manmade items within the deep sea will likely accumulate to increasing quantities. Here we report the litter abundance encountered at the Pacific abyssal nodule fields from the Peru Basin at 4150 m depth. An average density of 2.67 litter items/ha was observed. Litter composed of plastic was the most abundant followed by metal and glass. At least 58 % of the items observed could be linked to the research expeditions conducted in the area and appeared to be mostly accidental disposals from ships. The data gathered was used to address temporal trends in litter abundance as well as the impact of human on-site presence and return cruises in the context of future deep-sea mining efforts.

Massive occurrence of benthic plastic debris at the abyssal seafloor beneath the Kuroshio Extension, the North West Pacific.

The abyss (3500-6500 m) covers the bulk of the deep ocean floor yet little is known about the extent of plastic debris on the abyssal seafloor. Using video imagery we undertook a quantitative assessment of the debris present on the abyssal seafloor (5700-5800 m depth) beneath the Kuroshio Extension current system in the Northwest Pacific. This body of water is one of the major transit pathways for the massive amounts of debris that are entering the North Pacific Ocean from Asia. Shallower sites (1400-1500 m depth) were also investigated for comparison. The dominant type of debris was single-use plastics - mainly bags and food packaging. The density of the plastic debris (mean 4561 items/km2) in the abyssal zone was the highest recorded for an abyssal plain suggesting that the deep-sea basin in the Northwest Pacific is a significant reservoir of plastic debris.

Digenean parasites of deep-sea teleosts: A progress report.

The developments in the study of digeneans of deep-sea fish in the 21st Century are documented and discussed. Most recent work has been on the bathyal fauna (i.e. 1,000m-2,999 m depth), with virtually nothing on the abyssal fauna (i.e. deeper than 3,000 m). The one study on hydrothermal vent digeneans has indicated that these regions probably harbour a distinctive fauna. The demarcation of the deep-sea fauna is blurred at the poles, where the cold-adapted fauna appears similar to the shallower bathyal fauna. The abyssal fauna, however, appears distinct, possibly due to adaptations to variable or ultra-high pressures. The digenean fauna of bathypelagic fishes is depauperate. Recent phylogenetic studies reinforce the view that the typical deep-sea fauna has radiated in the deep-sea. Encroachment into the deep from shallow water is relatively rare. Overall, the digenean fauna in the deep-sea is distinctly less diverse that the equivalent fauna in shallow waters. A major conclusion is that our understanding of the deep-sea digenean fauna is poor, and that much further work over a much wider area is needed.

Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates a Complex Physical Structure.

Plant mitochondrial genomes vary widely in size. Although many plant mitochondrial genomes have been sequenced and assembled, the vast majority are of angiosperms, and few are of gymnosperms. Most plant mitochondrial genomes are smaller than a megabase, with a few notable exceptions. We have sequenced and assembled the complete 5.5-Mb mitochondrial genome of Sitka spruce (Picea sitchensis), to date, one of the largest mitochondrial genomes of a gymnosperm. We sequenced the whole genome using Oxford Nanopore MinION, and then identified contigs of mitochondrial origin assembled from these long reads based on sequence homology to the white spruce mitochondrial genome. The assembly graph shows a multipartite genome structure, composed of one smaller 168-kb circular segment of DNA, and a larger 5.4-Mb single component with a branching structure. The assembly graph gives insight into a putative complex physical genome structure, and its branching points may represent active sites of recombination.

Dark Ophiuroid Biodiversity in a Prospective Abyssal Mine Field.

The seafloor contains valuable mineral resources, including polymetallic (or manganese) nodules that form on offshore abyssal plains. The largest and most commercially attractive deposits are located in the Clarion Clipperton Fracture Zone (CCZ), in the eastern Pacific Ocean (EP) between Hawaii and Mexico, where testing of a mineral collection system is set to start soon [1]. The requirement to establish pre-mining environmental management plans has prompted numerous recent biodiversity and DNA barcoding surveys across these remote regions. Here we map DNA sequences from sampled ophiuroids (brittle stars, including post-larvae) of the CCZ and Peru Basin onto a substantial tree of life to show unprecedented levels of abyssal ophiuroid phylogenetic diversity including at least three ancient (>70 Ma), previously unknown clades. While substantial dark (unobserved) biodiversity has been reported from various microbial meta-barcoding projects [2, 3], our data show that we have considerably under-estimated the biodiversity of even the most conspicuous mega-faunal invertebrates [4] of the EP abyssal plain.

Accelerated freshening of Antarctic Bottom Water over the last decade in the Southern Indian Ocean.

Southern Ocean abyssal waters, in contact with the atmosphere at their formation sites around Antarctica, not only bring signals of a changing climate with them as they move around the globe but also contribute to that change through heat uptake and sea level rise. A repeat hydrographic line in the Indian sector of the Southern Ocean, occupied three times in the last two decades (1994, 2007, and, most recently, 2016), reveals that Antarctic Bottom Water (AABW) continues to become fresher (0.004 ± 0.001 kg/g decade-1), warmer (0.06° ± 0.01°C decade-1), and less dense (0.011 ± 0.002 kg/m3 decade-1). The most recent observations in the Australian-Antarctic Basin show a particularly striking acceleration in AABW freshening between 2007 and 2016 (0.008 ± 0.001 kg/g decade-1) compared to the 0.002 ± 0.001 kg/g decade-1 seen between 1994 and 2007. Freshening is, in part, responsible for an overall shift of the mean temperature-salinity curve toward lower densities. The marked freshening may be linked to an abrupt iceberg-glacier collision and calving event that occurred in 2010 on the George V/Adélie Land Coast, the main source region of bottom waters for the Australian-Antarctic Basin. Because AABW is a key component of the global overturning circulation, the persistent decrease in bottom water density and the associated increase in steric height that result from continued warming and freshening have important consequences beyond the Southern Indian Ocean.

Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation.

The genome sequences of the plastid and mitochondrion of white spruce (Picea glauca) were assembled from whole-genome shotgun sequencing data using ABySS. The sequencing data contained reads from both the nuclear and organellar genomes, and reads of the organellar genomes were abundant in the data as each cell harbors hundreds of mitochondria and plastids. Hence, assembly of the 123-kb plastid and 5.9-Mb mitochondrial genomes were accomplished by analyzing data sets primarily representing low coverage of the nuclear genome. The assembled organellar genomes were annotated for their coding genes, ribosomal RNA, and transfer RNA. Transcript abundances of the mitochondrial genes were quantified in three developmental tissues and five mature tissues using data from RNA-seq experiments. C-to-U RNA editing was observed in the majority of mitochondrial genes, and in four genes, editing events were noted to modify ACG codons to create cryptic AUG start codons. The informatics methodology presented in this study should prove useful to assemble organellar genomes of other plant species using whole-genome shotgun sequencing data.