Phylogenomics invokes the clade housing Cryptista, Archaeplastida, and Microheliella maris

As-yet-undescribed branches in the tree of eukaryotes are potentially represented by some of “orphan” protists (unicellular micro-eukaryotes), of which phylogenetic affiliations have not been clarified in previous studies. By clarifying the phylogenetic positions of orphan protists, we may fill the previous gaps in the diversity of eukaryotes and further uncover the novel affiliation between two (or more) major lineages in eukaryotes. Microheliella maris was originally described as a member of the phylum Heliozoa, but a pioneering large-scale phylogenetic analysis failed to place this organism within the previously described species/lineages with confidence. In this study, we analyzed a 319-gene alignment and demonstrated that M. maris represents a basal lineage of one of the major eukaryotic lineages, Cryptista. We here propose a new clade name “Pancryptista” for Cryptista plus M. maris. The 319-gene analyses also indicated that M. maris is a key taxon to recover the monophyly of Archaeplastida and the sister relationship between Archaeplastida and Pancryptista, which is collectively called as “CAM clade” here. Significantly, Cryptophyceae tend to be attracted to Rhodophyta depending on the taxon sampling (ex., in the absence of M. maris and Rhodelphidia) and the particular phylogenetic “signal” most likely hindered the stable recovery of the monophyly of Archaeplastida in previous studies. We hypothesize that many cryptophycean genes (including those in the 319-gene alignment) recombined partially with the homologous genes transferred from the red algal endosymbiont during secondary endosymbiosis and bear a faint phylogenetic affinity to the rhodophytan genes.

Complete Genome Sequence of Microbulbifer sp. YPW1 from Mangrove Sediments in Yanpu Harbor, China

In this work, a strain named YPW1 was isolated from the sediments of an artificial mangrove in Yanpu harbor, China. Whole genomic sequencing was conducted to reveal the potential ecological roles of strain YPW1 for the environment. The result of 16S rRNA gene alignment assigned strain YPW1 into Microbulbifer genus, and then, 10 representative genomes from Microbulbifer genus were selected to compare with YPW1. Results showed that the genome of strain YPW1 possessed more carbohydrate-active enzyme genes to transform various recalcitrant polysaccharides into bioavailable monosaccharides than those of the selected genomes. Furthermore, among the selected genomes, YPW1 was the only strain with nitrate, nitrite, and nitric oxide reductases which could appoint nitrous oxide, a powerful greenhouse gas, as the end-product of its denitrification process. Therefore, strain YPW1 was a member of Microbulbifer genus with special ecological roles that served as the center for the degradation and utilization of polysaccharides and the performer of denitrification with greenhouse gas as the end-product, and the abundance and biological activity of YPW1 could be an indicator to reflect the ecological function of this artificial mangrove in energy material providing and climate regulation.

1RS.1BL molecular resolution provides novel contributions to wheat improvement

SUMMARYWheat-rye 1RS.1BL translocation has a significant impact on wheat yield and hence food production globally. However, the genomic basis of its contributions to wheat improvement is undetermined. Here, we generated a high-quality assembly of 1RS.1BL translocation comprising 748,715,293 bp with 4,996 predicted protein-coding genes. We found the size of 1RS is larger than 1BS with the active centromere domains shifted to the 1RS side instead of the 1BL side in Aikang58 (AK58). The gene alignment showed excellent synteny with 1BS from wheat and genes from 1RS were expressed well in wheat especially for 1RS where expression was higher than that of 1BS for the grain-20DPA stage associated with greater grain weight and negative flour quality attributes. A formin-like-domain protein FH14 (TraesAK58CH1B01G010700) was important in regulating cell division. Two PPR genes were most likely the genes for the multi fertility restoration locus Rf multi. Our data not only provide the high-resolution structure and gene complement for the 1RS.1BL translocation, but also defined targets for enhancing grain yield, biotic and abiotic stress, and fertility restoration in wheat.

Which mammalian species are at risk of being infected by SARS-CoV-2: an ACE2 perspective

SARS-CoV-2 can transmit efficiently in humans, but it is less clear what other mammalian are at high risk of being infected. SARS-CoV-2 contain a Spike (S) protein that uses mammalian ACE2 receptors to mediate cell entry, a species with a human-like ACE2 receptor is therefore at risk of being infected by SARS-CoV-2. We compared between 131 mammalian ACE2 genes and 15 coronavirus S proteins. We showed that global similarity reflected by the phylogenetic relationship from ACE2 gene alignment is a poor predictor of high-risk mammals, whereas local ACE2 similarities at key binding sites highlight several high-risk mammals. Both SARS-CoV and SARS-CoV-2 likely have a bat origin; however, direct human transmission is unlikely due to their differences in ACE2 receptors, and various mammals share similar or better homologies in ACE2 receptor with humans. Furthermore, by comparing key binding sites at S protein of SARS-like coronaviruses in high-risk mammals, we found high similarities in S protein binding domains between SARS-CoV-2 and Pangolin-CoV but not Civets-CoV, and high similarities between SARS-CoV and Civets-CoV but not Pangolin-CoV. Hence, evolutionary adaptation of the bat virus in different intermediate hosts could allow it to acquire distinct high binding potential between S protein and human-like ACE2 receptors.

Homothallism, morphology and phylogenetic position of a new species of Sellaphora (Bacillariophyta), S. pausariae

Background and aims – The eutrophic Blackford Pond in Edinburgh has already provided the holotypes of six other Sellaphora species. A further undescribed species is present and requires description and characterization. Methods – Clones of the new species are characterized by light (LM) and scanning electron microscopy (SEM) and molecular phylogenetics (from a concatenated five-gene alignment of 18S rDNA, 28S rDNA, 23S rDNA, cox1 and rbcL, and a two-gene alignment of cox1 and rbcL). Key results – Sellaphora pausariae sp. nov. is named in honour of Dr Eileen Cox (‘pausaria’ = a lady coxswain). In molecular phylogenies, small-celled Sellaphora species (‘minima’ and ‘seminulum’ morphologies) branch off at the base of Sellaphora, though nodes are not well supported. Species and demes previously classified in either “Navicula pupula” or “Navicula bacillum” group into three very well supported clades (numbered 1–3). Although appearing in LM and SEM like a smaller, more delicate version of S. obesa, S. pausariae (clade 1) is not closely related to S. obesa (clade 2). Features of Sellaphora pausariae not confirmed previously in any Sellaphora but possibly widespread are: (a) hymenes with pores arranged in a regular scatter; (b) a stepped mantle near the poles; and (c) a ‘primodominant’ girdle comprising a wide band 1, a segmental band 2, and two extremely thin bands at the abvalvar end of the girdle. Sellaphora pausariae is homothallic; a deficiency of interclonal pairings in two-clone mixtures is interpreted as reflecting the tendency of cells to mate with their immediate neighbours. Conclusions – Morphologically, the new species can be differentiated from existing described species, though only problematically from some informally named demes. Molecularly, it is clearly characterized by the five genes sequenced. Girdle terminology needs expansion (e.g. to distinguish primodominant girdles from ‘graded’ ones, in which the bands gradually decrease in width and structural complexity from the valve outwards).

Fast Klebsiella pneumoniae typing for outbreak reconstruction: an highly discriminatory HRM protocol on wzi capsular gene developed using EasyPrimer tool

ABSTRACTIn this work we present EasyPrimer, a user-friendly online tool developed to assist pan-PCR and High Resolution Melting (HRM) primer design. The tool finds the most suitable regions for primer design in a gene alignment and returns a clear graphical representation of their positions on the gene. EasyPrimer is particularly useful in difficult contexts, e.g. on gene alignments of hundreds of sequences and/or on highly variable genes. HRM analysis is an emerging method for fast and cost saving bacterial typing and an HRM scheme of six primer sets on five Multi-Locus Sequence Type (MLST) genes is already available for Klebsiella pneumoniae. We validated the tool designing a scheme of two HRM primer sets on the hypervariable gene wzi of Klebsiella pneumoniae and compared the two schemes. The wzi scheme resulted to have a discriminatory power comparable to the HRM MLST scheme, using only one third of primer sets. Then we successfully used the wzi HRM primer scheme to reconstruct a Klebsiella pneumoniae nosocomial outbreak in few hours. The use of hypervariable genes reduces the number of HRM primer sets required for bacterial typing allowing to perform cost saving, large-scale surveillance programs.