Genetic Diversity Associated with Eco-geographical Parameters, Morphological Characteristics and Soil Analyzes of Common Vetch (Vicia sativa L.) in Algeria

Background: In the present study, we have set a goal, to study the genetic variability and phylogenetic affinities of 26 spontaneous Vicia sativa L. accessions collected in Algeria, as part of the recovery and enhancement of the local genetic heritage and its integration into the breeding and varietal creation programs. Methods: Morphological traits, performance parameters and phenological stages of each accession were tracked during an experimental test in pots under greenhouse conditions from December 29, 2019 to June 1, 2020. An eco-geographical characterization of samples was also carried out through geographical coordinates. On the other side and for the first time in Algeria, soil analyses of each site were undertaken. Result: The phylogenetic study of accessions confirm the taxonomic complexity of the group V. sativa L. According to the principal component analyses and kruskal-Wallis test, the most segregating variables with the highest values and the largest K variance ratios are most of the attributes associated with the flower, pod and seed. The association of the two dissimilarity matrix carried out by a Mantel test between the morphological and eco-geographic parameters showed a significant effect with a p value = 0.004 at the threshold of alpha=0.05 and a correlation coefficient r (AB) = 0.156.

The complete mitochondrial genomes of Notiophilus quadripunctatus Dejean, 1826 and Omophron limbatum (Fabricius, 1777): New insights into the mitogenome phylogeny of the Carabidae (Insecta, Coleoptera)

The Carabidae is by far the largest family of the Adephaga, with more than 40,000 described species. Whereas their phylogeny has been extensively studied, convergences and reversals in morphological traits prevent a robust phylogenetic concept so far. In this study, we sequenced the complete mitochondrial genomes of Notiophilus quadripunctatus (Nebriinae) and Omophrom limbatum (Omophroninae) using high-throughput sequencing. Both mitogenomes consisted of a single circular DNA molecule that encoded the typical 13 protein-coding genes, two subunits of mitochondrial RNAs, 22 tRNAs and a putative control region. Our phylogenetic study placed Omophrom limbatum as sister taxon to all other analyzed ground beetle species whereas Notiophilus quadripunctatus was identified as sister to Nebria brevicollis as part of the Nebriinae. The analyses also support the monophyly of the Cicindelidae but place Trachypachus holmbergi (Trachypachidae) within the Carabidae. Nevertheless, almost all carabid subfamilies with more than one analyzed species were identified as monophyla.

Problems and prospects of cultivation of indigenous rice landraces of Uttar Dinajpur, West Bengal, India with special reference to Tulaipanji

The district Uttar Dinajpur of West Bengal is bestowed with very fertile soil, which helps to grow paddy and other agricultural crops. Cultivation of indigenous rice has been practiced by farmers since ancient times. Indigenous rice has several socio-economic, ecological and genetical aspects but the major problem lies in their comparatively low output. The diversity of indigenous rice landraces has been drastically reduced due to the introduction of high yielding varieties (HYVs). Through extensive survey it has been found that about 74 indigenous rice land races were available in different blocks of the district, but among them only about 20 varieties are now in farmers' hand while more than 70% of them are not cultivated in practical field. In India, the indigenous aromatic rice landrace Tulaipanji (GI 530) is only grown in Raiganj sub-division of Uttar Dinajpur and small pockets of Dakshin Dinajpur district of West Bengal. Due to its aroma and quality this rice could make the position in global market through proper marketing. A phylogenetic study of the rice landraces has been performed and observed that only three of them i.e., Tulaipanji, Radhunipagal and Gobindavog are closely related to each other, which also has the close lineage with the Asian wild-rice (Oryza rufipogon). Today's society demands the interaction and incorporation of scientific technology for the upliftment of indigenous rice landrace sustainable cultivation. Really it has the immense scope and prospects, which ultimately save the human life from notorious diseases.

Molecular inference of subgenus Hermodactyloides Spach for vascular flora of Iraq

Iris reticulata of sect. Reticulata from subg. Hermodactyloides in Iraq have been circumscribed based on morphological characters long time ago. Recent work, carried out in neighbouring countries (Turkey and Iran), added the new sect. Zagrica, which includes four new species. No molecular study has been performed yet to confirm the status of this subgenus. In this work, a phylogenetic study of the subg. Hermodactyloides was carried out by using internal transcribed spacer (ITS) region as well as morphological traits, with the aim to examine this subgenus in Iraq. Molecular data indicate that a new section is diverged from Hermodachtyloides and should be added to vascular flora of Iraq as a second section named Zagrica. This outcome is consistent with the morphological description. This work also implies that leaf transverse section should be considered as main morphological characters to be taken into account to separate the Reticulata section from Zagrica which has the same taxonomical value as the position of ovary (above ground or subterranean).

Herzog Vindicated: Integrative Taxonomy Reveals that Trichostomum brachydontium (Pottiaceae, Bryophyta) Comprises Several Species

The morphologically variable moss Trichostomum brachydontium is very common in south and west Europe, particularly under Mediterranean and Atlantic climates. A morphological study was conducted alongside a molecular phylogenetic study based on nr ITS and cp rbcL regions in order to assess if T. brachydontium is an exceptionally polymorphic species as evidenced by the number of described infraspecific taxa from the last century or, alternatively, if it includes more than one species, and if so, to find the valid name for them. Phylogenetic analyses of both nuclear and chloroplast datasets show that there are four well-supported clades. While the ITS based tree is in good agreement with the morphological data, there are a few inconsistencies with reference to the rbcL tree; this may be explained by incomplete lineage sorting or by hybridization. The morphological survey revealed well-defined discriminate differences between the four phylogenetic lineages. The taxonomic conclusions include the recognition of four species: T. brachydontium s.s., T. herzogii (a new name proposed for var. cuspidatum), T. littorale and T. meridionale (a new name proposed for var. densum). Lectotypes are designated for T. brachydontium and T. littorale. Our results underline the ongoing need of integrative studies to examine further the underestimated diversity of the T. brachydontium complex in other regions.

Phylogenetic study of the genus Pohlia (Mielichhoferiaceae, Bryophyta) based on chloroplast DNA sequences

The phylogenetic circumscription and taxonomic status of the genus Pohlia in the Mniaceae sensu lato was investigated based on chloroplast DNA sequences (rbcL, rps4, and trnL-F), with a focus on species occurring in Japan. The maximum likelihood and Bayesian inference analyses of sequences obtained from 34 species of Mniaceae s.l., including 13 Pohlia species, suggested that the genus Pohlia and the family Mielichhoferiaceae are not monophyletic in their present circumscription, but confirmed that the family Mniaceae is monophyletic in its traditional sense. These results are congruent with previous molecular phylogenetic studies. Three distinct clades were recognized in the Mielichhoferiaceae, almost corresponding to three sections of Pohlia (Pohlia, Cacodon and Apalodictyon). One of them branched off first within the Mniaceae s.l., and the other two were sister to the remainder of the Mniaceae s.l. The single included Schizymenium formed a monophyletic group with Pohlia sect. Pohlia and Epipterygium with Pohlia sect. Apalodictyon, confirming the results of previous studies. The results indicate that the taxonomic status of the genus Pohlia and family Mielichhoferiaceae are in need of revision. Phylogenetic analyses nested the accessions of P. camptotrachela within P. annotina and P. flexuosa clades, highlighting the need for taxonomic revision of Japanese propaguliferous Pohlia species.

Phenotypic and Genomic Comparison of Klebsiella pneumoniae Lytic Phages: vB_KpnM-VAC66 and vB_KpnM-VAC13

Klebsiella pneumoniae is a human pathogen that worsens the prognosis of many immunocompromised patients. Here, we annotated and compared the genomes of two lytic phages that infect clinical strains of K. pneumoniae (vB_KpnM-VAC13 and vB_KpnM-VAC66) and phenotypically characterized vB_KpnM-VAC66 (time of adsorption of 12 min, burst size of 31.49 ± 0.61 PFU/infected cell, and a host range of 20.8% of the tested strains). Transmission electronic microscopy showed that vB_KpnM-VAC66 belongs to the Myoviridae family. The genomic analysis of the phage vB_KpnM-VAC66 revealed that its genome encoded 289 proteins. When compared to the genome of vB_KpnM-VAC13, they showed a nucleotide similarity of 97.56%, with a 93% of query cover, and the phylogenetic study performed with other Tevenvirinae phages showed a close common ancestor. However, there were 21 coding sequences which differed. Interestingly, the main differences were that vB_KpnM-VAC66 encoded 10 more homing endonucleases than vB_KpnM-VAC13, and that the nucleotidic and amino-acid sequences of the L-shaped tail fiber protein were highly dissimilar, leading to different three-dimensional protein predictions. Both phages differed significantly in their host range. These viruses may be useful in the development of alternative therapies to antibiotics or as a co-therapy increasing its antimicrobial potential, especially when addressing multidrug resistant (MDR) pathogens.

Transcriptome of the synganglion and characterization of the cys-loop ligand-gated ion channel gene family in the tick Ixodes ricinus.

Ticks represent a major health issue for humans and domesticated animals. Assessing the expression patterns of the tick's central nervous system, known as the synganglion, is an important step in understanding tick physiology and in managing tick-borne diseases. Neuron-specific genes like the cys-loop ligand-gated ion channels (cys-loop LGICs) are important pharmacological targets of acaricides. Here, we carried out the sequencing of transcriptomes of the I. ricinus synganglion, for adult ticks in different conditions (unfed males, unfed females, and partially-fed females). The de novo assembly of these transcriptomes allowed us to obtain a large collection of cys-loop LGICs sequences. A reference meta-transcriptome based on synganglion and whole body transcriptomes was then produced, showing high completeness and allowing differential expression analyses between synganglion and whole body. Many of the genes upregulated in the synganglion were related to biological processes or functions associated with neurotransmission and located in neurones or the synaptic membrane, including most of the cys-loop LGICs. As a first step of a functional study of cysLGICs, we cloned the predicted sequence of the resistance to dieldrin (RDL) subunit homologue, and functionally reconstituted the first GABA-gated receptor of Ixodes ricinus using a hetrologous expression approach. A phylogenetic study was performed for the nicotinic acetylcholine receptors (nAChRs) and for other cys-loop LGICs respectively, showing tick-specific expansions of some types of receptors (Histamine-gated, GluCls).

A New and Expanded Phylogenetic Analysis of Hyptidinae (Ocimeae-Lamiaceae)

Abstract— Hyptidinae, ca. 400 species, is an important component of Neotropical vegetation formations. Members of the subtribe possess flowers arranged in variously modified bracteolate cymes and nutlets with an expanded areole and all share a unique explosive mechanism of pollen release, except for Asterohyptis. In a recent phylogenetic study, the group had its generic delimitations rearranged with the recognition of 19 genera in the subtribe. Although the previous phylogenetic analysis covered almost all the higher taxa in the subtribe, it lacked a broader sampling at the species level. Here we present a new expanded phylogenetic analysis for the subtribe comprising 153 accessions of Hyptidinae sequenced for the nuclear nrITS, nrETS, and waxy regions and the plastid markers trnL-F, trnS-G, trnD-T, and matK. Our results widely support the previous phylogenetic results with some changes in the support and relationship between genera. It also uncovers the need for a new combination of Eriope machrisae in Hypenia and the phylogenetic position of Hyptis sect. Rhytidea, which was demonstrated to be part of Mesosphaerum. The generic delimitation in Hyptidinae is discussed, and we recommend that further studies with more markers are needed to confirm the monophyly of Hyptidendron and Mesosphaerum, as well as to support taxonomic changes on the infrageneric delimitation within Hyptis s. s.

Reconciliation of evidence for the Portulacineae “backbone” phylogeny

Portulacineae comprise a clade of eight ostensibly monophyletic families, four of which (Anacampserotaceae, Montiaceae, Portulacaceae s. str., and Talinaceae) and part of a fifth (Didiereaceae) had been classified traditionally in Portulacaceae s. lato. The clade also includes Basellaceae, Cactaceae, and Halophytaceae. While available evidence strongly supports recognition of major clades within Portulacineae, current analyses disagree with respect to relations among them, such that the Portulacineae “backbone” phylogeny remains “unresolved.” The disagreements might owe in part to incongruent data and/or poor analysis and/or known theoretical shortcomings of the analytical methods. But I argue here that it reflects mostly the failure to appreciate the fundamental property of living organisms, viz. their inherent determinism consequent to autopoiesis. This property renders the evolutionary process as idiosyncratic. This, in turn, renders phylogeny inherently unpredictable and, strictly speaking, unrecoverable. I also emphasize that the hierarchical organization of organisms predicts that phylogeny should not be strictly tree-like. Nonetheless, evolutionary history is materially tangible, hence is within the realm of scientific inquiry. I make two proposals here. One is that (often futile) efforts to resolve phylogeny as a tree reflect a constitutive cognitive proclivity to resolve trees even when phylogeny is not tree-like and/or otherwise “resolvable.” To mitigate this tendency, I propose that the objective of phylogenetic study should be reconciliation rather than resolution. In this way, the lack of tree-like phylogenetic resolution becomes useful knowledge. In this theoretical framework, I evaluate what can be considered tentatively known about the Portulacineae backbone phylogeny.