Reference-free discovery of nuclear SNPs permits accurate, sensitive identification of Carya (hickory) species and hybrids.

PREMISE: DNA-based species identification is critical when morphological identification is restricted, but DNA-based identification pipelines typically rely on the ability to compare homologous sequence data across species. Because many clades lack robust genomic resources, we present here a bioinformatics pipeline capable of generating genome-wide single-nucleotide polymorphism (SNP) data while circumventing the need for any reference genome or annotation data. METHODS: Using the SISRS bioinformatics pipeline, we generated de novo ortholog data for the genus Carya, isolating sites where genetic variation was restricted to a single Carya species (i.e., species-informative SNPs). We leveraged these SNPs to identify both full-species and hybrid Carya specimens, even at very low sequencing depths. RESULTS: We identified between 46,000 and 476,000 species-identifying SNPs for each of eight diploid Carya species, and all species identifications were concordant with the species of record. For all putative F1 hybrid specimens, both parental species were correctly identified in all cases, and more punctate patterns of introgression were detectable in more cryptic crosses. DISCUSSION: Bioinformatics pipelines that use only short-read sequencing data provide vital new tools enabling rapid expansion of DNA identification assays for model and non-model clades alike.

Using RDNA sequences to define dinoflagellate species.

Dinoflagellate species are traditionally defined using morphological characters, but molecular evidence accumulated over the past several decades indicates many morphologically-based descriptions are inaccurate. This recognition led to an increasing reliance on DNA sequence data, particularly rDNA gene segments, in defining species. The validity of this approach assumes the divergence in rDNA or other selected genes parallels speciation events. Another concern is whether single gene rDNA phylogenies by themselves are adequate for delineating species or if multigene phylogenies are required instead. Currently, few studies have directly assessed the relative utility of multigene versus rDNA-based phylogenies for distinguishing species. To address this, the current study examined D1-D3 and ITS/5.8S rDNA gene regions, a multi-gene phylogeny, and morphological characters in Gambierdiscus and other related dinoflagellate genera to determine if they produce congruent phylogenies and identify the same species. Data for the analyses were obtained from previous sequencing efforts and publicly available dinoflagellate transcriptomic libraries as well from the additional nine well-characterized Gambierdiscus species transcriptomic libraries generated in this study. The D1-D3 and ITS/5.8S phylogenies successfully identified the described Gambierdiscus and Alexandrium species. Additionally, the data showed that the D1-D3 and multigene phylogenies were equally capable of identifying the same species. The multigene phylogenies, however, showed different relationships among species and are likely to prove more accurate at determining phylogenetic relationships above the species level. These data indicated that D1-D3 and ITS/5.8S rDNA region phylogenies are generally successful for identifying species of Gambierdiscus, and likely those of other dinoflagellates. To assess how broadly general this finding is likely to be, rDNA molecular phylogenies from over 473 manuscripts representing 232 genera and 863 described species of dinoflagellates were reviewed. Results showed the D1-D3 rDNA and ITS phylogenies in combination are capable of identifying 97% of dinoflagellate species including all the species belonging to the genera Alexandrium, Ostreopsis and Gambierdiscus, although it should be noted that multi-gene phylogenies are preferred for inferring relationships among these species. A protocol is presented for determining when D1-D3, confirmed by ITS/5.8S rDNA sequence data, would take precedence over morphological features when describing new dinoflagellate species. This protocol addresses situations such as: a) when a new species is both morphologically and molecularly distinct from other known species; b) when a new species and closely related species are morphologically indistinguishable, but genetically distinct; and c) how to handle potentially cryptic species and cases where morphotypes are clearly distinct but have the same rDNA sequence. The protocol also addresses other molecular, morphological, and genetic approaches required to resolve species boundaries in the small minority of species where the D1-D3/ITS region phylogenies fail.

Suitability of DNA Sequencing Tools for Identifying Edible Seaweeds Sold in the United States.

Seaweeds have been consumed by billions of people around the world and are increasingly popular in United States (US) diets. Some seaweed species have been associated with adverse health effects-such as heavy metal toxicity-and higher priced seaweeds may be more prone to adulteration. Knowing which species of seaweeds are being marketed in the US is important for protecting human health and preventing economic adulteration. Therefore, the United States Food and Drug Administration is developing new DNA-based species identification tools to complement established chemical methods for verifying the accurate labeling of products. Here, seaweed products available in the United States were surveyed using a tiered approach to evaluate a variety of DNA extraction techniques followed by traditional DNA barcoding via Sanger sequencing; if needed, genome skimming of total extracted nuclear DNA via next-generation sequencing was performed. This two-tiered approach of DNA barcoding and genome skimming could identify most seaweed samples (41/46), even those in blends (2/2, 1 out of 3 labeled species in each). Only two commercial samples appeared to be mislabeled or to contain unintended algal species. Five samples, labeled as "hijiki" or "arame", could not be confirmed by these DNA-based identification methods.

Full Chloroplast Genome Sequence of the Economically Important Dietary Supplement and Spice Curcuma longa.

Curcuma longa L. is a native species of Asia that is commonly known as turmeric. It is a spice also used in traditional medicine to treat a wide range of illnesses. Here, we present the fully annotated chloroplast genome of Curcuma longa.

Microbial Diversity in the Eukaryotic SAR Clade: Illuminating the Darkness Between Morphology and Molecular Data.

Despite their diversity and ecological importance, many areas of the SAR-Stramenopila, Alveolata, and Rhizaria-clade are poorly understood as the majority (90%) of SAR species lack molecular data and only 5% of species are from well-sampled families. Here, we review and summarize the state of knowledge about the three major clades of SAR, describing the diversity within each clade and identifying synapomorphies when possible. We also assess the "dark area" of SAR: the morphologically described species that are missing molecular data. The majority of molecular data for SAR lineages are characterized from marine samples and vertebrate hosts, highlighting the need for additional research effort in areas such as freshwater and terrestrial habitats and "non-vertebrate" hosts. We also describe the paucity of data on the biogeography of SAR species, and point to opportunities to illuminate diversity in this major eukaryotic clade. See also the video abstract here: https://youtu.be/_VUXqaX19Rw.

A Tale of Transmission: Aeromonas veronii Activity within Leech-Exuded Mucus.

Transmission, critical to the establishment and persistence of host-associated microbiotas, also exposes symbionts to new environmental conditions. With horizontal transmission, these different conditions represent major lifestyle shifts. Yet genome-wide analyses of how microbes adjust their transcriptomes toward these dramatic shifts remain understudied. Here, we provide a comprehensive and comparative analysis of the global transcriptional profiles of a symbiont as it shifts between lifestyles during transmission. The gammaproteobacterium Aeromonas veronii is transmitted from the gut of the medicinal leech to other hosts via host mucosal castings, yet A. veronii can also transition from mucosal habitancy to a free-living lifestyle. These three lifestyles are characterized by distinct physiological constraints and consequently lifestyle-specific changes in the expression of stress-response genes. Mucus-bound A. veronii had the greatest expression in terms of both the number of loci and levels of transcription of stress-response mechanisms. However, these bacteria are still capable of proliferating within the mucus, suggesting the availability of nutrients within this environment. We found that A. veronii alters transcription of loci in a synthetic pathway that obtains and incorporates N-acetylglucosamine (NAG; a major component of mucus) into the bacterial cell wall, enabling proliferation. Our results demonstrate that symbionts undergo dramatic local adaptation, demonstrated by widespread transcriptional changes, throughout the process of transmission that allows them to thrive while they encounter new environments which further shape their ecology and evolution.

Draft Genome Sequence of Pedobacter sp. Strain Hv1, an Isolate from Medicinal Leech Mucosal Castings.

The Pedobacter sp. Hv1 strain was isolated from the medicinal leech, Hirudo verbana, mucosal castings. These mucosal sheds have been demonstrated to play a role in horizontal symbiont transmission. Here, we report the draft 4.9 Mbp genome sequence of Pedobacter sp. strain Hv1.

Hitchhiking of host biology by beneficial symbionts enhances transmission.

Transmission plays a key role in the evolution of symbiosis. Mixed mode transmission combines horizontal and vertical mechanisms for symbiont acquisition. However, features that enable mixed transmission are poorly understood. Here, we determine the mechanistic basis for the recruitment of the beneficial bacterium, Aeromonas veronii by the leech, Hirudo verbana. We demonstrate that host mucosal secretions complement imperfect symbiont vertical transmission. First, we show that the A. veronii population within secretions originates from the host digestive tract and proliferates synchronously with shedding frequency, demonstrating the coupling of partner biology. Furthermore, leeches are attracted to these castings with oral contact proving sufficient for symbiont transmission. Leech attraction to mucus is not affected by the symbiont state of either the host or mucus, suggesting that A. veronii exploits preexisting host behavior and physiological traits. A dual transmission mode, integrating multiple layers of host contributions, may prove evolutionarily advantageous for a wide range of symbioses. Using such a strategy, host infection is ensured, while also providing access to a higher genetic diversity of symbionts. Countless host-associated microbes exhibit mixed mode transmission, supporting the use of the leech symbiosis as a model for enhancing our understanding of the specificity, establishment and persistence of microbiotas.

Characterization of shed medicinal leech mucus reveals a diverse microbiota.

Microbial transmission through mucosal-mediated mechanisms is widespread throughout the animal kingdom. One example of this occurs with Hirudo verbana, the medicinal leech, where host attraction to shed conspecific mucus facilitates horizontal transmission of a predominant gut symbiont, the Gammaproteobacterium Aeromonas veronii. However, whether this mucus may harbor other bacteria has not been examined. Here, we characterize the microbiota of shed leech mucus through Illumina deep sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. Additionally, Restriction Fragment Length Polymorphism (RFLP) typing with subsequent Sanger Sequencing of a 16S rRNA gene clone library provided qualitative confirmation of the microbial composition. Phylogenetic analyses of full-length 16S rRNA sequences were performed to examine microbial taxonomic distribution. Analyses using both technologies indicate the dominance of the Bacteroidetes and Proteobacteria phyla within the mucus microbiota. We determined the presence of other previously described leech symbionts, in addition to a number of putative novel leech-associated bacteria. A second predominant gut symbiont, the Rikenella-like bacteria, was also identified within mucus and exhibited similar population dynamics to A. veronii, suggesting persistence in syntrophy beyond the gut. Interestingly, the most abundant bacterial genus belonged to Pedobacter, which includes members capable of producing heparinase, an enzyme that degrades the anticoagulant, heparin. Additionally, bacteria associated with denitrification and sulfate cycling were observed, indicating an abundance of these anions within mucus, likely originating from the leech excretory system. A diverse microbiota harbored within shed mucus has significant potential implications for the evolution of microbiomes, including opportunities for gene transfer and utility in host capture of a diverse group of symbionts.