scholarly journals Insights on Lulworthiales Inhabiting the Mediterranean Sea and Description of Three Novel Species of the Genus Paralulworthia

2021 ◽  
Vol 7 (11) ◽  
pp. 940
Author(s):  
Anna Poli ◽  
Valeria Prigione ◽  
Elena Bovio ◽  
Iolanda Perugini ◽  
Giovanna Cristina Varese
Keyword(s):  
Mediterranean Sea ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Posidonia Oceanica ◽  
Protein Coding ◽  
Biotechnological Potential ◽  
Protein Coding Genes ◽  
Wide Range ◽  
The Mediterranean ◽  
Bayesian Phylogeny

The order Lulworthiales, with its sole family Lulworthiaceae, consists of strictly marine genera found on a wide range of substrates such as seagrasses, seaweeds, and seafoam. Twenty-one unidentified Lulworthiales were isolated in previous surveys aimed at broadening our understanding of the biodiversity hosted in the Mediterranean Sea. Here, these organisms, mostly found in association with Posidonia oceanica and with submerged woods, were examined using thorough multi-locus phylogenetic analyses and morphological observations. Maximum-likelihood and Bayesian phylogeny based on nrITS, nrSSU, nrLSU, and four protein-coding genes led to the introduction of three novel species of the genus Paralulworthia: P. candida, P. elbensis, and P. mediterranea. Once again, the marine environment is a confirmed huge reservoir of novel fungal lineages with an under-investigated biotechnological potential waiting to be explored.

scholarly journals Corollospora mediterranea: A Novel Species Complex in the Mediterranean Sea

2021 ◽  
Vol 11 (12) ◽  
pp. 5452
Author(s):  
Anna Poli ◽  
Elena Bovio ◽  
Iolanda Perugini ◽  
Giovanna Cristina Varese ◽  
Valeria Prigione
Keyword(s):  
Mediterranean Sea ◽  
Oil Spill ◽  
Species Complex ◽  
Novel Species ◽  
Posidonia Oceanica ◽  
Fungal Species ◽  
Biotechnological Potential ◽  
The Mediterranean ◽  
Bayesian Phylogeny ◽  
A New Species

The genus Corollospora, typified by the arenicolous fungus Corollospora maritima, consists of twenty-five cosmopolitan species that live and reproduce exclusively in marine environments. Species of this genus are known to produce bioactive compounds and can be potentially exploited as bioremediators of oil spill contaminated beaches; hence their biotechnological importance. In this paper, nine fungal strains isolated in the Mediterranean Sea, from the seagrass Posidonia oceanica (L.) Delile, from driftwood and seawater contaminated by an oil spill, were investigated. The strains, previously identified as Corollospora sp., were examined by deep multi-loci phylogenetic and morphological analyses. Maximum-likelihood and Bayesian phylogeny based on seven genetic markers led to the introduction of a new species complex within the genus Corollospora: Corollospora mediterranea species complex (CMSC). The Mediterranean Sea, once again, proves an extraordinary reservoir of novel fungal species with a still undiscovered biotechnological potential.

scholarly journals Sequence Variation in Two Protein-Coding Genes Correlates with Mycelial Compatibility Groupings in Sclerotium rolfsii

2013 ◽  
Vol 103 (5) ◽  
pp. 479-487 ◽  
Author(s):  
Efrén Remesal ◽  
Blanca B. Landa ◽  
María del Mar Jiménez-Gasco ◽  
Juan A. Navas-Cortés
Keyword(s):  
Rna Polymerase Ii ◽  
Sequence Variation ◽  
Geographic Origin ◽  
Sclerotium Rolfsii ◽  
Nuclear Ribosomal Dna ◽  
Causal Organism ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Wide Range ◽  
Mycelial Compatibility

Populations of Sclerotium rolfsii, the causal organism of Sclerotium root-rot on a wide range of hosts, can be placed into mycelial compatibility groups (MCGs). In this study, we evaluated three different molecular approaches to unequivocally identify each of 12 previously identified MCGs. These included restriction fragment length polymorphism (RFLP) patterns of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (rDNA) and sequence analysis of two protein-coding genes: translation elongation factor 1α (EF1α) and RNA polymerase II subunit two (RPB2). A collection of 238 single-sclerotial isolates representing 12 MCGs of S. rolfsii were obtained from diseased sugar beet plants from Chile, Italy, Portugal, and Spain. ITS-RFLP analysis using four restriction enzymes (AluI, HpaII, RsaI, and MboI) displayed a low degree of variability among MCGs. Only three different restriction profiles were identified among S. rolfsii isolates, with no correlation to MCG or to geographic origin. Based on nucleotide polymorphisms, the RPB2 gene was more variable among MCGs compared with the EF1α gene. Thus, 10 of 12 MCGs could be characterized utilizing the RPB2 region only, while the EF1α region resolved 7 MCGs. However, the analysis of combined partial sequences of EF1α and RPB2 genes allowed discrimination among each of the 12 MCGs. All isolates belonging to the same MCG showed identical nucleotide sequences that differed by at least in one nucleotide from a different MCG. The consistency of our results to identify the MCG of a given S. rolfsii isolate using the combined sequences of EF1α and RPB2 genes was confirmed using blind trials. Our study demonstrates that sequence variation in the protein-coding genes EF1α and RPB2 may be exploited as a diagnostic tool for MCG typing in S. rolfsii as well as to identify previously undescribed MCGs.

Mitogenome of Alaudala cheleensis (Passeriformes: Alaudidae) and comparative analyses of Sylvioidea mitogenomes

Zootaxa ◽  
2021 ◽  
Vol 4952 (2) ◽  
pp. 331-353
Author(s):  
CHAO YANG ◽  
LE ZHAO ◽  
QINGXIONG WANG ◽  
HAO YUAN ◽  
XUEJUAN LI ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Gene Order ◽  
Phylogenetic Relationships ◽  
Gene Rearrangement ◽  
Phylogenetic Analyses ◽  
Protein Coding ◽  
Comparative Analyses ◽  
Protein Coding Genes ◽  
Basal Position

To gain a better understanding of mitogenome features and phylogenetic relationships in Sylvioidea, a superfamily of Passerida, suborder Passeri, Passeriformes, the whole mitogenome of Alaudala cheleensis Swinhoe (Alaudidae) was sequenced, a comparative mitogenomic analysis of 18 Sylvioidea species was carried out, and finally, a phylogeny was reconstructed based on the mitochondrial dataset. Gene order of the A. cheleensis mitogenome was similar to that of other Sylvioidea species, including the gene rearrangement of cytb-trnT-CR1-trnP-nad6-trnE-remnant CR2-trnF-rrnS. There was slightly higher A+T content than that of G+C in the mitogenome, with an obvious C skew. The ATG codon initiated all protein-coding genes, while six terminating codons were used. The secondary structure of rrnS contained three domains and 47 helices, whereas rrnL included six domains and 60 helices. All tRNAs could be folded into a classic clover-leaf secondary structure except for trnS (AGY). The CR1 could be divided into three domains, including several conserved boxes (C-string, F, E, D, C and B-box, Bird similarity box, CSB1). Comparative analyses within Sylvioidea mitogenomes showed that most mitochondrial features were consistent with that of the A. cheleensis mitogenome. The basal position of the Alaudidae within the Sylvioidea in our phylogenetic analyses is consistent with other recent studies. 

scholarly journals Ophelia roscoffensis Augener, 1910: a new polychaete record in Italian waters

Check List ◽  
2019 ◽  
Vol 15 (3) ◽  
pp. 489-495
Author(s):  
Emanuele Mancini ◽  
Francesco Tiralongo ◽  
Daniele Ventura ◽  
Andrea Bonifazi
Keyword(s):  
Mediterranean Sea ◽  
First Record ◽  
Posidonia Oceanica ◽  
Tyrrhenian Sea ◽  
The Mediterranean

Ophelia roscoffensis Augener, 1910 is an opheliid worm identifiable by the number of anterior abranchiate chaetigers and the number of the gill pairs. Although it was already reported in the Mediterranean Sea, it has never been found in the Italian waters. This study represents the first record of Ophelia roscoffensis in the Italian waters. A total of 18 specimens were collected along the coast of Civitavecchia (Tyrrhenian Sea) in a Posidonia oceanica (L.) Delile bed at a depth of 7 m.

scholarly journals Goniadella bobrezkii (Annenkova, 1929) (Annelida, Polychaeta): first record in the Italian waters

Check List ◽  
2019 ◽  
Vol 15 (1) ◽  
pp. 125-130
Author(s):  
Emanuele Mancini ◽  
Francesco Tiralongo ◽  
Daniele Ventura ◽  
Andrea Bonifazi
Keyword(s):  
Mediterranean Sea ◽  
First Record ◽  
Posidonia Oceanica ◽  
Posterior Spine ◽  
The Mediterranean ◽  
Italian Coasts

Goniadella bobrezkii (Annenkova, 1929) is a small goniadid worm identifiable by the number of anterior uniramous parapodia and by the position of the posterior spine-like notochetae arising dorsal to dorsal cirri. Although it was already reported in the Mediterranean Sea, it has never been found in the Italian waters. This study represents the first generic and specific record of G. bobrezkii along Italian coasts. A total of 25 specimens were collected in a Posidonia oceanica (L.) Delile bed, depth of 7 m, off Civitavecchia (Rome).

scholarly journals Is Posidonia oceanica regression a general feature in the Mediterranean Sea?

2013 ◽  
Vol 14 (1) ◽  
pp. 193 ◽  
Author(s):  
M. BONACORSI ◽  
C. PERGENT-MARTINI ◽  
N. BREAND ◽  
G. PERGENT
Keyword(s):  
Mediterranean Sea ◽  
Temporal Evolution ◽  
Posidonia Oceanica ◽  
Aerial Photographs ◽  
Human Pressure ◽  
The Mediterranean ◽  
Spatio Temporal ◽  
Mapping Techniques ◽  
Significant Regression ◽  
Ancient Maps

Over the last few years, a widespread regression of Posidonia oceanica meadows has been noticed in the Mediterranean Sea. However, the magnitude of this decline is still debated. The objectives of this study are (i) to assess the spatio-temporal evolution of Posidonia oceanica around Cap Corse (Corsica) over time comparing available ancient maps (from 1960) with a new (2011) detailed map realized combining different techniques (aerial photographs, SSS, ROV, scuba diving); (ii) evaluate the reliability of ancient maps; (iii) discuss observed regression of the meadows in relation to human pressure along the 110 km of coast. Thus, the comparison with previous data shows that, apart from sites clearly identified with the actual evolution, there is a relative stability of the surfaces occupied by the seagrass Posidonia oceanica. The recorded differences seem more related to changes in mapping techniques. These results confirm that in areas characterized by a moderate anthropogenic impact, the Posidonia oceanica meadow has no significant regression and that the changes due to the evolution of mapping techniques are not negligible. However, others facts should be taken into account before extrapolating to the Mediterranean Sea (e.g. actually mapped surfaces) and assessing the amplitude of the actual regression.

scholarly journals Phylogenetic relationships and taxonomic position of genus Hyperacrius (Rodentia: Arvicolinae) from Kashmir based on evidences from analysis of mitochondrial genome and study of skull morphology

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10364
Author(s):  
Natalia I. Abramson ◽  
Fedor N. Golenishchev ◽  
Semen Yu. Bodrov ◽  
Olga V. Bondareva ◽  
Evgeny A. Genelt-Yanovskiy ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Morphological Characters ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Skull Morphology ◽  
Protein Coding ◽  
Protein Coding Genes

In this article, we present the nearly complete mitochondrial genome of the Subalpine Kashmir vole Hyperacrius fertilis (Arvicolinae, Cricetidae, Rodentia), assembled using data from Illumina next-generation sequencing (NGS) of the DNA from a century-old museum specimen. De novo assembly consisted of 16,341 bp and included all mitogenome protein-coding genes as well as 12S and 16S RNAs, tRNAs and D-loop. Using the alignment of protein-coding genes of 14 previously published Arvicolini tribe mitogenomes, seven Clethrionomyini mitogenomes, and also Ondatra and Dicrostonyx outgroups, we conducted phylogenetic reconstructions based on a dataset of 13 protein-coding genes (PCGs) under maximum likelihood and Bayesian inference. Phylogenetic analyses robustly supported the phylogenetic position of this species within the tribe Arvicolini. Among the Arvicolini, Hyperacrius represents one of the early-diverged lineages. This result of phylogenetic analysis altered the conventional view on phylogenetic relatedness between Hyperacrius and Alticola and prompted the revision of morphological characters underlying the former assumption. Morphological analysis performed here confirmed molecular data and provided additional evidence for taxonomic replacement of the genus Hyperacrius from the tribe Clethrionomyini to the tribe Arvicolini.

Additions to Ochroconis from India

Phytotaxa ◽  
2019 ◽  
Vol 427 (3) ◽  
pp. 186-199
Author(s):  
ARCHANA SINGH ◽  
NIKHIL KUMAR SINGH ◽  
PARAS NATH SINGH ◽  
RAGHVENDRA SINGH ◽  
NAWAL KISHORE DUBEY
Keyword(s):  
New Species ◽  
Medicinal Plant ◽  
Ribosomal Dna ◽  
Leaf Surface ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Nuclear Ribosomal Dna ◽  
Monophyletic Clade ◽  
Protein Coding

Ochroconis helicteris, a novel species of the oligotrophic genus Ochroconis (Sympoventuriaceae, Venturiales), has been described and illustrated. Morphologically, this species has characters similar to allied species in the genus Ochroconis, but differs in conidial dimensions and shape. Phylogenetic analyses using nuclear ribosomal DNA gene ITS and protein coding gene BT2 revealed it clustering as monophyletic clade which was separated from known Ochroconis species. New species was isolated from leaf surface of medicinal plant Helicteris isora L.

scholarly journals LncExpDB: an expression database of human long non-coding RNAs

2020 ◽  
Vol 49 (D1) ◽  
pp. D962-D968 ◽  
Author(s):  
Zhao Li ◽  
Lin Liu ◽  
Shuai Jiang ◽  
Qianpeng Li ◽  
Changrui Feng ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Biological Functions ◽  
Protein Coding ◽  
Web Interfaces ◽  
Functional Studies ◽  
Protein Coding Genes ◽  
Genes Expression ◽  
Wide Range ◽  
Non Coding Rnas ◽  
User Friendly

Abstract Expression profiles of long non-coding RNAs (lncRNAs) across diverse biological conditions provide significant insights into their biological functions, interacting targets as well as transcriptional reliability. However, there lacks a comprehensive resource that systematically characterizes the expression landscape of human lncRNAs by integrating their expression profiles across a wide range of biological conditions. Here, we present LncExpDB (https://bigd.big.ac.cn/lncexpdb), an expression database of human lncRNAs that is devoted to providing comprehensive expression profiles of lncRNA genes, exploring their expression features and capacities, identifying featured genes with potentially important functions, and building interactions with protein-coding genes across various biological contexts/conditions. Based on comprehensive integration and stringent curation, LncExpDB currently houses expression profiles of 101 293 high-quality human lncRNA genes derived from 1977 samples of 337 biological conditions across nine biological contexts. Consequently, LncExpDB estimates lncRNA genes’ expression reliability and capacities, identifies 25 191 featured genes, and further obtains 28 443 865 lncRNA-mRNA interactions. Moreover, user-friendly web interfaces enable interactive visualization of expression profiles across various conditions and easy exploration of featured lncRNAs and their interacting partners in specific contexts. Collectively, LncExpDB features comprehensive integration and curation of lncRNA expression profiles and thus will serve as a fundamental resource for functional studies on human lncRNAs.

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