scholarly journals Phylogenetic and evolutionary relationships in selected Pinus species using rbcL and matK chloroplast genes

2021 ◽  
pp. 064-068
Author(s):  
Singh Lav ◽  
Dixit Pooja ◽  
Srivastava Ravi Prakash ◽  
Pandey Shivaraman ◽  
Singh Arpit ◽  
...  
Keyword(s):  
Evolutionary Relationships ◽  
Chloroplast Genes ◽  
Pinus Species

scholarly journals Characterizing gene tree conflict in plastome-inferred phylogenies

2019 ◽  
Author(s):  
Joseph F. Walker ◽  
Gregory W. Stull ◽  
Nathanael Walker-Hale ◽  
Oscar M. Vargas ◽  
Drew A. Larson
Keyword(s):  
Amino Acids ◽  
Evolutionary Rate ◽  
Gene Tree ◽  
Phylogeny Reconstruction ◽  
Evolutionary Relationships ◽  
Gene Length ◽  
Chloroplast Genes ◽  
Protein Coding ◽  
Angiosperm Phylogeny ◽  
Molecule Type

ABSTRACTPremise of the studyEvolutionary relationships among plants have been inferred primarily using chloroplast data. To date, no study has comprehensively examined the plastome for gene tree conflict.MethodsUsing a broad sampling of angiosperm plastomes, we characterized gene tree conflict among plastid genes at various time scales and explore correlates to conflict (e.g., evolutionary rate, gene length, molecule type).Key resultsWe uncover notable gene tree conflict against a backdrop of largely uninformative genes. We find gene length is the strongest correlate to concordance, and that nucleotides outperform amino acids. Of the most commonly used markers, matK greatly outperforms rbcL; however, the rarely used gene rpoC2 is the top-performing gene in every analysis. We find that rpoC2 reconstructs angiosperm phylogeny as well as the entire concatenated set of protein-coding chloroplast genes.ConclusionsOur results suggest that longer genes are superior for phylogeny reconstruction. The alleviation of some conflict through the use of nucleotides suggests that systematic error is likely the root of most of the observed conflict, but further research on biological conflict within plastome is warranted given the documented cases of heteroplasmic recombination. We suggest rpoC2 as a useful marker for reconstructing angiosperm phylogeny, reducing the effort and expense of assembling and analyzing entire plastomes.

scholarly journals Repression of Essential Chloroplast Genes Reveals New Signaling Pathways and Regulatory Feedback Loops in Chlamydomonas

2013 ◽  
Vol 25 (1) ◽  
pp. 167-186 ◽  
Author(s):  
Silvia Ramundo ◽  
Michèle Rahire ◽  
Olivier Schaad ◽  
Jean-David Rochaix
Keyword(s):  
Signaling Pathways ◽  
Feedback Loops ◽  
Chloroplast Genes

Monosaccharide Biosynthesis Pathways Database

Glycobiology ◽  
2021 ◽  
Author(s):  
Jaya Srivastava ◽  
P Sunthar ◽  
Petety V Balaji
Keyword(s):  
Expression Profiling ◽  
Experimental Studies ◽  
Structural Complexity ◽  
Evolutionary Relationships ◽  
Enzyme Assays ◽  
Biosynthesis Pathway ◽  
Knock Out ◽  
Set Up ◽  
Function Relationship ◽  
Natural Glycans

Abstract A distinctive feature of glycans vis-à-vis proteins and nucleic acids is its structural complexity which arises from the huge repertoire of monosaccharides, isomeric linkages and branching. A very large number of monosaccharides have so far been discovered in natural glycans. Experimentally, pathways for the biosynthesis have been characterized completely for 55 monosaccharides and partially for a few more. However, there is no single platform which provides information about monosaccharide biosynthesis pathways and associated enzymes We have gathered 572 experimentally characterized enzymes of 66 biosynthesis pathways from literature and set up a first of its kind database called the Monosaccharide Biosynthesis Pathways Database http://www.bio.iitb.ac.in/mbpd/). Annotations such as the reaction catalysed, substrate specificity, biosynthesis pathway and PubMed IDs are provided for all the enzymes in the database. Sequence homologs of the experimentally characterized enzymes found in nearly 13,000 completely sequenced genomes from Bacteria and Archaea have also been included in the database. This platform will help in the deduction of evolutionary relationships among enzymes such as aminotransferases, nucleotidyltransferases, acetyltransferases and SDR family enzymes. It can also facilitate experimental studies such as direct enzyme assays to validate putative annotations, establish structure–function relationship, expression profiling to determine the function, determine the phenotypic consequences of gene knock-out/knock-in and complementation studies.

scholarly journals A new lineage of mazaediate fungi in the Eurotiomycetes: Cryptocaliciomycetidae subclass. nov., based on the new species Cryptocalicium blascoi and the revision of the ascoma evolution

2021 ◽  
Vol 20 (7) ◽  
pp. 889-904
Author(s):  
M. Prieto ◽  
Javier Etayo ◽  
I. Olariaga
Keyword(s):  
New Species ◽  
Common Ancestor ◽  
External Surface ◽  
Evolutionary Relationships ◽  
New Order ◽  
Ancestral State ◽  
Multigene Phylogeny ◽  
State Reconstruction ◽  
Distinct Structure ◽  
Dark Violet

AbstractThe class Eurotiomycetes (Ascomycota, Pezizomycotina) comprises important fungi used for medical, agricultural, industrial and scientific purposes. Eurotiomycetes is a morphologically and ecologically diverse monophyletic group. Within the Eurotiomycetes, different ascoma morphologies are found including cleistothecia and perithecia but also apothecia or stromatic forms. Mazaediate representatives (with a distinct structure in which loose masses of ascospores accumulate to be passively disseminated) have evolved independently several times. Here we describe a new mazaediate species belonging to the Eurotiomycetes. The multigene phylogeny produced (7 gene regions: nuLSU, nuSSU, 5.8S nuITS, mtSSU, RPB1, RPB2 and MCM7) placed the new species in a lineage sister to Eurotiomycetidae. Based on the evolutionary relationships and morphology, a new subclass, a new order, family and genus are described to place the new species: Cryptocalicium blascoi. This calicioid species occurs on the inner side of loose bark strips of Cupressaceae (Cupressus, Juniperus). Morphologically, C. blascoi is characterized by having minute apothecioid stalked ascomata producing mazaedia, clavate bitunicate asci with hemiamyloid reaction, presence of hamathecium and an apothecial external surface with dark violet granules that becomes turquoise green in KOH. The ancestral state reconstruction analyses support a common ancestor with open ascomata for all deep nodes in Eurotiomycetes and the evolution of closed ascomata (cleistothecioid in Eurotiomycetidae and perithecioid in Chaetothyriomycetidae) from apothecioid ancestors. The appropriateness of the description of a new subclass for this fungus is also discussed.

scholarly journals Annelid Diversity: Historical Overview and Future Perspectives

Diversity ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 129
Author(s):  
María Capa ◽  
Pat Hutchings
Keyword(s):  
State Of The Art ◽  
Molecular Taxonomy ◽  
Evolutionary Relationships ◽  
Diverse Group ◽  
Future Perspectives ◽  
Special Issue ◽  
Species Numbers ◽  
Species Complexes ◽  
Taxonomic Groups ◽  
A New Species

Annelida is a ubiquitous, common and diverse group of organisms, found in terrestrial, fresh waters and marine environments. Despite the large efforts put into resolving the evolutionary relationships of these and other Lophotrochozoa, and the delineation of the basal nodes within the group, these are still unanswered. Annelida holds an enormous diversity of forms and biological strategies alongside a large number of species, following Arthropoda, Mollusca, Vertebrata and perhaps Platyhelminthes, among the species most rich in phyla within Metazoa. The number of currently accepted annelid species changes rapidly when taxonomic groups are revised due to synonymies and descriptions of a new species. The group is also experiencing a recent increase in species numbers as a consequence of the use of molecular taxonomy methods, which allows the delineation of the entities within species complexes. This review aims at succinctly reviewing the state-of-the-art of annelid diversity and summarizing the main systematic revisions carried out in the group. Moreover, it should be considered as the introduction to the papers that form this Special Issue on Systematics and Biodiversity of Annelids.

scholarly journals Ophiocordyceps salganeicola, a parasite of social cockroaches in Japan and insights into the evolution of other closely-related Blattodea-associated lineages

IMA Fungus ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
João P. M. Araújo ◽  
Mitsuru G. Moriguchi ◽  
Shigeru Uchiyama ◽  
Noriko Kinjo ◽  
Yu Matsuura
Keyword(s):  
Genetic Similarity ◽  
Evolutionary History ◽  
Fungal Species ◽  
Evolutionary Relationships ◽  
Ryukyu Archipelago ◽  
Phylogenetic Placement ◽  
The Social ◽  
Host Jump ◽  
High Degree ◽  
A New Species

AbstractThe entomopathogenic genus Ophiocordyceps includes a highly diverse group of fungal species, predominantly parasitizing insects in the orders Coleoptera, Hemiptera, Hymenoptera and Lepidoptera. However, other insect orders are also parasitized by these fungi, for example the Blattodea (termites and cockroaches). Despite their ubiquity in nearly all environments insects occur, blattodeans are rarely found infected by filamentous fungi and thus, their ecology and evolutionary history remain obscure. In this study, we propose a new species of Ophiocordyceps infecting the social cockroaches Salganea esakii and S. taiwanensis, based on 16 years of collections and field observations in Japan, especially in the Ryukyu Archipelago. We found a high degree of genetic similarity between specimens from different islands, infecting these two Salganea species and that this relationship is ancient, likely not originating from a recent host jump. Furthermore, we found that Ophiocordyceps lineages infecting cockroaches evolved around the same time, at least twice, one from beetles and the other from termites. We have also investigated the evolutionary relationships between Ophiocordyceps and termites and present the phylogenetic placement of O. cf. blattae. Our analyses also show that O. sinensis could have originated from an ancestor infecting termite, instead of beetle larvae as previously proposed.

scholarly journals Resolving Phylogenetic Relationships within Passeriformes Based on Mitochondrial Genes and Inferring the Evolution of Their Mitogenomes in Terms of Duplications

2019 ◽  
Vol 11 (10) ◽  
pp. 2824-2849 ◽  
Author(s):  
Paweł Mackiewicz ◽  
Adam Dawid Urantówka ◽  
Aleksandra Kroczak ◽  
Dorota Mackiewicz
Keyword(s):  
Phylogenetic Analyses ◽  
Mitochondrial Genes ◽  
The Other ◽  
Phylogenetic Position ◽  
Evolutionary Relationships ◽  
Mitochondrial Genomes ◽  
Ancestral State ◽  
Phylogenetic Information ◽  
Long Time ◽  
Tree Topologies

Abstract Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass.

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