Phylogenomic position of eupelagonemids, abundant, and diverse deep-ocean heterotrophs

Eupelagonemids, formerly known as Deep Sea Pelagic Diplonemids I (DSPD I), are among the most abundant and diverse heterotrophic protists in the deep ocean, but little else is known about their ecology, evolution, or biology in general. Originally recognized solely as a large clade of environmental ribosomal subunit RNA gene sequences (SSU rRNA), branching with a smaller sister group DSPD II, they were postulated to be diplonemids, a poorly studied branch of Euglenozoa. Although new diplonemids have been cultivated and studied in depth in recent years, the lack of cultured eupelagonemids has limited data to a handful of light micrographs, partial SSU rRNA gene sequences, a small number of genes from single amplified genomes, and only a single formal described species, Eupelagonema oceanica. To determine exactly where this clade goes in the tree of eukaryotes and begin to address the overall absence of biological information about this apparently ecologically important group, we conducted single-cell transcriptomics from two eupelagonemid cells. A SSU rRNA gene phylogeny shows that these two cells represent distinct subclades within eupelagonemids, each different from E. oceanica. Phylogenomic analysis based on a 125-gene matrix contrasts with the findings based on ecological survey data and shows eupelagonemids branch sister to the diplonemid subgroup Hemistasiidae.

Two new species of Antrodia (Polyporales, Basidiomycota) in western China

Two new species of Antrodia, A. aridula and A. variispora, are described from western China. Phylogeny based on a six-gene dataset (ITS + nLSU + nSSU + mtSSU + TEF1 + RPB2) demonstrates that samples of the two species form two independent lineages within the clade of Antrodia s.s. and are different in morphology from the existing species of Antrodia. Antrodia aridula is characterized by its annual and resupinate basidiocarps with angular to irregular pores of 2-3 mm each and oblong ellipsoid to cylindrical basidiospores measuring 9-12 × 4.2-5.3 μm, growing on gymnosperm wood in a dry environment. Antrodia variispora is characterized by its annual and resupinate basidiocarps with sinuous or dentate pores with a size of 1-1.5 mm each and oblong ellipsoid, fusiform, pyriform, or cylindrical basidiospores measuring 11.5-16 × 4.5-5.5 μm, growing on the wood of Picea. The differences between the new species and morphologically similar species are discussed in this article.

Improving plant productivity by re-tuning the regeneration of RuBP in the Calvin-Benson-Bassham cycle

The Calvin-Benson-Bassham (CBB) cycle is arguably the most important pathway on earth, capturing CO₂ from the atmosphere and converting it into organic molecules, providing the basis for life on our planet. This cycle has been intensively studied over the 50 yr since it was elucidated, and it is highly conserved across nature, from cyanobacteria to the largest of our land plants. Eight out of the 11 enzymes in this cycle catalyse the regeneration of ribulose-1-5 bisphosphate (RuBP), the CO₂ acceptor molecule. The potential to manipulate RuBP regeneration to improve photosynthesis has been demonstrated in a number of plant species, and the development of new technologies, such as omics and synthetic biology provides exciting future opportunities to improve photosynthesis and increase crop yields.

Antigenic diversity of MASP gene family of Trypanosoma cruzi

Trypanosoma cruzi, the etiological agent of Chagas disease (CD), is a heterogeneous species with high genetic and phenotypic diversity. MASP is the second largest multigene family of T. cruzi. The high degree of polymorphism of the family associated with its location at the surface of infective forms of T. cruzi suggests that MASP participates in mechanisms of host-parasite interaction. In this work, MASP members were divided into 7 subgroups based on protein sequence similarity, and one representative member from each subgroup was chosen to be expressed recombinantly. Immunogenicity of recombinant MASP proteins (rMASP) was investigated using different sera panels from T. cruzi infected mice. To mimic a natural condition in which different MASP members are expressed at the same time in the parasite population, a multiplex bead-based flow cytometry assay was also standardized. Results showed that rMASPs are poorly recognized by sera from mice infected with Colombiana strain, whereas sera from mice infected with CL Brener and Y display high reactivity against the majority of rMASPs tested. Flow cytometry showed that MASP recognition profile changes 10 days after infection. Also, multiplex assay suggests that MASP M1 and M2 are more immunogenic than the other MASP members evaluated that may play an immunodominant role during infection.

Mitochondrial and Plastid Genomes of the Monoraphid Diatom Schizostauron trachyderma

We provide for the first time the complete plastid and mitochondrial genomes of a monoraphid diatom: Schizostauron trachyderma. The mitogenome is 41,957 bp in size and displays two group II introns in the cox1 gene. The 187,029 bp plastid genome features the typical quadripartite architecture of diatom genomes. It contains a group II intron in the petB gene that overlaps the large single-copy and the inverted repeat region. There is also a group IB4 intron encoding a putative LAGLIDADG homing endonuclease in the rnl gene. The multigene phylogenies conducted provide more evidence of the proximity between S. trachyderma and fistula-bearing species of biraphid diatoms.

Novel species of Pestalotiopsis fungi on Dracaena from Thailand

A survey of the diversity and distribution of microfungi on Dracaena leaf litter in Songkhla Province (Thailand) yielded two collections of pestalotiopsis-like fungi. Analyses of a combined ITS, TEF1-α and TUB2 sequence data matrix were applied to infer the phylogenetic position of these new isolates in Pestalotiopsis. The phylogenies indicated that these two isolates were monophyletic and constituted a distinct lineage that perceived a taxonomic novelty in Pestalotiopsis. This clade shared a close phylogenetic affinity with P. adusta, P. krabiensis, P. pandanicola and P. papuana. The comparison of morphological features with the phylogenetically closely related taxa are given and the new species is introduced as Pestalotiopsis dracaenicola sp. nov. with comprehensive descriptions and illustrations herein.

Does the Gonostomum-patterned oral apparatus in hypotrichia carry a phylogenetic signal? Evidence from morphological and molecular data based on extended taxon sampling using three nuclear genes (Ciliophora, Spirotrichea)

The classification of hypotrichs based on the gonostomatid oral structure is widely accepted, but the phylogenetic signal of this character is unknown. Here, we infer the species phylogeny of those gonostomatids for which molecular data are available, plus 26 new sequences of SSU-rDNA, ITS1-5.8S-ITS2 and LSU-rDNA genes. The results indicate that: (i) the endoral is more phylogenetically informative than the paroral; (ii) the structure of the endoral and the Gonostomum-pattern adoral zone of membranelles are plesiomorphies for the hypotrichs sensu stricto; (iii) the group of species possessing these features is monophyletic in all our phylogenetic analyses, except that for the SSU-rDNA; (iv) Schmidingerotrichidae is monophyletic in all trees, suggesting that it is a well-defined family; (v) the Gonostomatidae is polyphyletic in the SSU-rDNA and ITS1-5.8S-ITS2 trees, with Gonostomum, Cladotricha, Cotterillia, Metagonostomum, Paragonostomum and Wallackia distributed among separate clades, but monophyletic in the LSU-rDNA and concatenated trees; (vi) higher hypotrich taxa such as core urostyloids and core sporadotrichids/stichotrichids might have evolved from species that possessed a gonostomatid oral apparatus.

Psychosocial problems in women attending French, German and Spanish genetics clinics before and after targeted or multigene testing results: an observational prospective study

OBJECTIVES AND SETTING

Advances in multigene panel testing for cancer susceptibility has increased the complexity of counselling, requiring particular attention to counselees' psychosocial needs. Changes in psychosocial problems before and after genetic testing were prospectively compared between genetic test results in women tested for breast or ovarian cancer genetic susceptibility in French, German and Spanish clinics.

PARTICIPANTS AND MEASURES

Among 752 counselees consecutively approached, 646 (86%) were assessed after the initial genetic consultation (T1), including 510 (68%) affected with breast cancer, of which 460 (61%) were assessed again after receiving the test result (T2), using questionnaires addressing genetic-specific psychosocial problems (Psychosocial Aspects of Hereditary Cancer (PAHC)-six scales). Sociodemographic and clinical data were also collected.

RESULTS

Seventy-nine (17.2%), 19 (4.1%), 259 (56.3%), 44 (9.6%) and 59 (12.8%) women received a BRCA1/2, another high/moderate-risk pathogenic variant (PV), negative uninformative, true negative (TN) or variant of uncertain significance result (VUS), respectively. On multiple regression analyses, compared with women receiving another result, those with a VUS decreased more in psychosocial problems related to hereditary predisposition (eg, coping with the test result) (ß=-0.11, p<0.05) and familial/social issues (eg, risk communication) (ß=-0.13, p<0.05), almost independently from their problems before testing. Women with a PV presented no change in hereditary predisposition problems and, so as women with a TN result, a non-significant increase in familial/social issues. Other PAHC scales (ie, emotions, familial cancer, personal cancer and children-related issues) were not affected by genetic testing.

CONCLUSIONS

In women tested for breast or ovarian cancer genetic risk in European genetics clinics, psychosocial problems were mostly unaffected by genetic testing. Apart from women receiving a VUS result, those with another test result presented unchanged needs in counselling in particular about hereditary predisposition and familial/social issues.

Metabarcoding using multiplexed markers increases species detection in complex zooplankton communities

Metabarcoding combines DNA barcoding with high-throughput sequencing, often using one genetic marker to understand complex and taxonomically diverse samples. However, species-level identification depends heavily on the choice of marker and the selected primer pair, often with a trade-off between successful species amplification and taxonomic resolution. We present a versatile metabarcoding protocol for biomonitoring that involves the use of two barcode markers (COI and 18S) and four primer pairs in a single high-throughput sequencing run, via sample multiplexing. We validate the protocol using a series of 24 mock zooplanktonic communities incorporating various levels of genetic variation. With the use of a single marker and single primer pair, the highest species recovery was 77%. With all three COI fragments, we detected 62%-83% of species across the mock communities, while the use of the 18S fragment alone resulted in the detection of 73%-75% of species. The species detection level was significantly improved to 89%-93% when both markers were used. Furthermore, multiplexing did not have a negative impact on the proportion of reads assigned to each species and the total number of species detected was similar to when markers were sequenced alone. Overall, our metabarcoding approach utilizing two barcode markers and multiple primer pairs per barcode improved species detection rates over a single marker/primer pair by 14% to 35%, making it an attractive and relatively cost-effective method for biomonitoring natural zooplankton communities. We strongly recommend combining evolutionary independent markers and, when necessary, multiple primer pairs per marker to increase species detection (i.e., reduce false negatives) in metabarcoding studies.

New Fusarium species from the Kruger National Park, South Africa

Three new Fusarium species, F. convolutans, F. fredkrugeri, and F. transvaalense (Ascomycota, Hypocreales, Nectriaceae) are described from soils collected in a catena landscape on a research supersite in the Kruger National Park, South Africa. The new taxa, isolated from the rhizosphere of three African herbaceous plants, Kyphocarpa angustifolia, Melhania acuminata, and Sida cordifolia, are described and illustrated by means of morphological and multilocus molecular analyses based on sequences from five DNA loci (CAL, EF-1 α, RPB1, RPB2 and TUB). According to phylogenetic inference based on Maximum-likelihood and Bayesian approaches, the newly discovered species are distributed in the Fusarium buharicum, F. fujikuroi, and F. sambucinum species complexes.

Molecular characterization of gliadins of Chinese Spring wheat in relation to celiac disease elicitors

The wheat seed storage proteins gliadin and glutenin are encoded by multigenes. Gliadins are further classified into α-, γ-, δ- and ω-gliadins. Genes encoding α-gliadins belong to a large multigene family, whose members are located on the homoeologous group 6 chromosomes at the Gli-2 loci. Genes encoding other gliadins are located on the homoeologous group 1 chromosomes at the Gli-1 loci. Two-dimensional polyacrylamide gel electrophoresis (2-DE) was used to characterize and profile the gliadins. The gliadins in aneuploid Chinese Spring wheat lines were then compared in this study. Gliadin proteins separated into 70 spots after 2-DE and a total of 10, 10 and 16 spots were encoded on chromosomes 6A, 6B and 6D, respectively, which suggested that they were α-gliadins. Similarly, six, three and seven spots were encoded on chromosomes 1A, 1B and 1D, respectively, which indicated that they were γ-gliadins. Spots that could not be assigned to chromosomes were N-terminally sequenced and were all determined to be α-gliadins or γ-gliadins. The 2-DE profiles showed that specific α-gliadin spots assigned to chromosome 6D were lost in tetrasomic chromosome 2A lines. Furthermore, western blotting against the Glia-α9 peptide, an epitope for celiac disease (CD), suggested that α-gliadins harboring the CD epitope on chromosome 6D were absent in the tetrasomic chromosome 2A lines. Systematic analysis of α-gliadins using 2-DE, quantitative RT-PCR and genomic PCR revealed that tetrasomic 2A lines carry deletion of a chromosome segment at the Gli-D2 locus. This structural alteration at the Gli-D2 locus may provide a genetic resource in breeding programs for the reduction of CD immunotoxicity.

Molecular evolution of the cecropin multigene family in silkworm Bombyx mori

Cecropins constitute one of the largest and most potent immune protein families found in insect species with diversified numbers and features. In view of the large number of cecropin proteins existing with much sequence variations among them, an overview of the multigene cecropin family in silkworm Bombyx mori was attempted in this study. Cecropin encodes an inducible 64 residue anti‐bacterial peptide and was clustered into two groups; first group viz. A and second group including B, D, E and Enbocin. Cecropin A consisted of two sub-groups located on chromosome number 6 of B.mori genome. Cecropin B consisted of six sub‐groups, cecropin D and E of one each and Enbocin of two. The second sub‐group formed in tandem array of multigene family locus over a length of 78.62 kb on chromosome number 26 in B.mori genome and was organized in positive as well as opposite orientation. The results indicated that cecropin B genes were organized in a close cluster with the intergenic sequence ranging from 1366 bp to 23526 bp. Interestingly a distantly related cecropin E was also located within the cecropin B multigene locus. Similarly distant members like cecropin D and Enbocin were also located in the 3’ region of cecropin B locus. The maximum intergenic region of 23526 bp observed between Cecropin D and Enbocin indicates that the two genes were distantly evolved. The phylogenetic analysis clearly indicates a positive correlation between the clusters and physical location on the chromosome, as the length of the intergenic region plays a major role to create newer cecropin families. EST database analysis suggests that most of the cecropin A members were expressed in the microbial fat body while, the cecropin B was equally expressed in fat body and other target tissues. The signal peptides were conserved in all the twelve paralogous gene sequences.