A single nucleotide variant in the PPARγ-homolog Eip75B affects fecundity in Drosophila

ABSTRACTStill little is understood about the nucleotide changes that underlie variation in complex phenotypes. Variation in the PPARγ-homolog Eip75B has previously been suggested to be associated with longevity and life-history differences in the fruit fly Drosophila melanogaster. Using RNAi knockdown, we first demonstrate that reduced expression of Eip75B in adults affects lifespan, egg laying rate and egg volume. To then test the effect of a naturally occurring SNP variant within a cis-regulatory domain of Eip75B, we screened wildtype lines with alternative alleles and conducted precise genome editing using CRISPR/Cas9. These experiments revealed that this natural polymorphism has a significant effect on fecundity and egg-to-adult viability, but not on longevity or other life-history traits. These results provide a rare functional validation for the role of a natural allelic variant in adaptation of life-history traits directly linked to fitness at the single nucleotide level.

Marine gregarine genomes illuminate current understanding of apicomplexan glideosome

Apicomplexans, parasite protists of a very wide diversity of metazoan hosts, are mostly known from species infecting human. Absence or limited data for basal lineages prevents a comprehensive view of evolutionary history and adaptive capacities of Apicomplexa. Here, we characterized the genome of the marine eugregarine Porospora gigantea, remarkable for the gigantic size of its vegetative feeding forms (trophozoites) and their speed of gliding movement, the fastest so far recorded for an Apicomplexa. Not a single but two highly related genomes named A and B were assembled. Highly syntenic, of similar size (9 Mb) and coding capacities (~5300 genes), they display a 10.8% divergence at nucleotide level corresponding to 16-38 My divergent time. Orthogroups analyses across 25 (proto)Apicomplexa including Gregarina niphandrodes showed that A and B are highly divergent from all other known apicomplexan species, revealing an unexpected diversity. These two related species branch in phylogenetic studies at the base of Cephaloidophoroidea, forming a new family in these crustacean gregarines. Gliding proteins data mining found a strong conservation of actin-related proteins, as well as of regulatory factors, within apicomplexan. In contrast, the conservation of core glideosome proteins and adhesion proteins appears to be highly variable among apicomplexan lineages, especially in gregarines. These results confirm the importance of studying gregarines to widen our biological and evolutionary view of apicomplexan parasites, to better apprehend species diversity and revise our understanding of the molecular bases of some key functions such as observed for the glideosome.

5-methylcytosine profiles in mouse transcriptomes suggest the randomness of m5C formation catalyzed by RNA methyltransferase

5-methylcytosine (m5C) is a type of chemical modification on the nucleotides and is widespread in both DNA and RNA. Although the DNA m5C has been extensively studied over the past years, the distribution and biological function of RNA m5C still remain to be elucidated. Here, I explored the profiles of RNA m5C in four mouse tissues and found that the methylation rates of cytosine were the same with the averages of methylation level at single-nucleotide level. Furthermore, I gave a mathematical formula to describe the observed relationship and analyzed it deeply. The sufficient necessary condition for the given formula suggests that the methylation levels at most m5C sites are the same in four mouse tissues. Therefore, I proposed a hypothesis that the m5C formation catalyzed by RNA methyltransferase is random and with the same probability at most m5C sites, which is the methylation rate of cytosine. My hypothesis can be used to explain the observed profiles of RNA m5C in four mouse tissues and will be benefit to future studies of the distribution and biological function of RNA m5C in mammals.

Complete Genome Sequence of Two Isolates of Spiraea Yellow Leafspot Virus (Genus: Badnavirus) From Spiraea x Bumalda ‘Anthony Waterer’

Isolates of spiraea yellow leafspot virus (SYLSV) were collected from Spiraea (Spiraea x bumalda) ‘Anthony Waterer’ plants showing virus-like symptoms including yellow spotting and leaf deformation in Minnesota and Maryland. The complete genome sequence of SYLSV-MN (Minnesota) and SYLSV-MD (Maryland) was 8,017bp in length. The sequences share 95% of identity at the nucleotide level. Both isolates have the same genome organization containing three open reading frames (ORFs), with ORF3 being the largest encoding the putative polyprotein of 232 kDa with conserved domains including Zinc finger, pepsin-like aspartate protease, reverse transcriptase (RT), and RNase H. Pairwise comparisons between members of the genus badnavirus showed that Gooseberry vein banding associated virus GB1 (HQ852248) and Rubus yellow net virus isolate Baumforth's Seedling A (KM078034) were the closest related virus sequences to SYLSV sharing 73% of identity at the nucleotide level. Bacilliform virions with dimensions of 150 nm x 30 nm were observed in virus preparations from symptomatic but not in asymptomatic plants.

A novel synonymous homozygous variant [c.2538G>A (p.Thr846Thr)] in TRPM6 in a patient with hypomagnesemia with secondary hypocalcemia

Objectives Hypomagnesemia 1, intestinal (HOMG1) is characterized by neurological symptoms that occur due to hypocalcemia and hypomagnesemia and caused by mutations in the TRPM6. Most of the identified variants in TRPM6 lead to premature termination: nonsense, frameshift, deletion, and splice site mutations. Case presentation Herein, we report a 1.5 month-old case who presented with convulsion due to hypocalcemia and hypomagnesemia in the early infancy. Sequencing of TRPM6 revealed a novel homozygous synonymous variant [c.2538G > A (p.Thr846Thr)] in the last codon of exon 19, which is most likely to affect the splicing. We report a novel homozygous synonymous variant in the TRPM6 leading to HOMG1, expanding the mutational spectrum. Conclusions Synonymous mutations that were previously considered as harmless should be evaluated at the nucleotide level, keeping in mind that they may affect splicing and cause to the disease.

StrainGE: A toolkit to track and characterize low-abundance strains in complex microbial communities

Human-associated microbial communities comprise not only complex mixtures of bacterial species, but also mixtures of conspecific strains, the implications of which are mostly unknown since strain level dynamics are underexplored due to the difficulties of studying them. We introduce the Strain Genome Explorer (StrainGE) toolkit, which deconvolves strain mixtures and characterizes component strains at the nucleotide level from short-read metagenomic sequencing with higher sensitivity and resolution than other tools. StrainGE is able to identify nearest known references and find variants for multiple conspecific strains within a sample at relative abundances below 0.1% in typical metagenomic datasets.

Novel transferable resistance-nodulation-division pump gene cluster tmexCD2-toprJ2 that confers tigecycline resistance in Raoultella ornithinolytica

We recently identified a novel plasmid-mediated RND-type efflux pump gene cluster, tmexCD1-toprJ1 in Klebsiella pneumoniae, that conferred resistance to multiple antimicrobials, including tigecycline. While homologs of tmexCD1-toprJ1 were found encoded in many other bacterial species in GenBank, their function and transfer mechanism remain unknown. This study identified another mobile gene cluster, tmexCD2-toprJ2, co-occurring on both plasmid (pHNNC189-2) and chromosome of a clinical Raoultella ornithinolytica strain NC189 producing KPC-2, NDM-1, and RmtC. tmexCD2-toprJ2 shares high similarity at nucleotide level to tmexCD1-toprJ1 with 98.02%, 96.75%, and 99.93% identity, respectively. Phylogenetic analysis revealed that tmexCD2-toprJ2 may have originated from chromosome of a Pseudomonas species. Expression of tmexCD2-toprJ2 in Escherichia coli strain resulted in an 8-fold increase of tigecycline MIC and decreased susceptibility to other antimicrobials. Genetic context analyses demonstrated that tmexCD2-toprJ2, together with the adjacent hypothetical site-specific integrase genes, was possibly captured and mobilized by a XerD-like tyrosine recombinase system, forming a putative transposition unit (xerD-like-int-thf2-ybjD-umuD-ΔumuC1-int1-int2-hp1-hp2-tnfxB2-ISBvi2-tmexCD2-toprJ2-ΔumuC1), which was inserted into umuC-like genes in both the NC189 plasmid pHNNC189-2 and chromosome. As tmexCD1-toprJ1 and tmexCD2-toprJ2 could confer multidrug resistance, the spread of these gene clusters, associated with the new recombinase system, calls for more attention.

Development of a Subtyping Tool for Zoonotic Pathogen Cryptosporidium Canis

Cryptosporidium canis is an important cause of cryptosporidiosis in canines and humans. Studies of the transmission characteristics of C. canis are currently hampered by lack of suitable subtyping tools. In this study, we conducted a genomic survey of the pathogen and developed a subtyping tool targeting the partial 60-kDa glycoprotein (gp60) gene. Seventy-six isolates previously identified as C. canis were analyzed using the new subtyping tool. Amplicons of expected size were obtained from 49 isolates, and phylogenetic analysis identified 10 subtypes clustered in five distinct groups (XXa–XXe). The largest group XXa contained 43 isolates from four subtypes that differed slightly from each other at the nucleotide level, while groups XXb–XXe contain one to three isolates each. The similar distribution of subtypes in humans and canines suggests that zoonotic transmission might play an important role in the epidemiology of C. canis. In addition, a suspected zoonotic transmission of C. canis between dogs and humans in a household was confirmed using the subtyping tool. The subtyping tool and data generated in this study might improve our understanding of the transmission of this zoonotic pathogen.