scholarly journals Mitogenomics and mitochondrial gene phylogeny decipher the evolution of Saccharomycotina yeasts

2021 ◽  
Author(s):  
Anastasia C Christinaki ◽  
Spyros G Kanellopoulos ◽  
Alexandra M Kortsinoglou ◽  
Bart Theelen ◽  
Teun Boekhout ◽  
...  
Keyword(s):  
Genetic Code ◽  
Genome Size ◽  
Genetic Recombination ◽  
Mitochondrial Gene ◽  
Molecular Dating ◽  
Phylogenetic Studies ◽  
Intergenic Regions ◽  
Size Diversity ◽  
Phylogenetic Lineages ◽  
Mt Genome

Saccharomycotina yeasts contain diverse clades within the kingdom of Fungi and are important to human everyday life. This work investigates the evolutionary relationships among these yeasts from a mitochondrial (mt) genomic perspective. A comparative study of 141 yeast mt genomes representing all major phylogenetic lineages of Saccharomycotina was performed, including genome size and content variability, intron and intergenic regions' diversity, genetic code alterations and syntenic variation. Findings from this study suggest that mt genome size diversity is the result of a ceaseless random process mainly based on genetic recombination and intron mobility. Gene order analysis revealed conserved syntenic units and many occurring rearrangements, which can be correlated with major evolutionary events as shown by the phylogenetic analysis of the concatenated mt protein matrix. For the first time, molecular dating indicated a slower mt genome divergence rate in the early stages of yeast evolution, in contrast with a faster rate in the late evolutionary stages, compared to their nuclear time divergence. Genetic code reassignments of mt genomes are a perpetual process happening in many different parallel evolutionary steps throughout Saccharomycotina evolution. Overall, this work shows that phylogenetic studies that employ the mt genome of yeasts highlight major evolutionary events.

First estimates of genome size in ribbon worms (phylum Nemertea) using flow cytometry and Feulgen image analysis densitometry

2014 ◽  
Vol 92 (10) ◽  
pp. 847-851 ◽  
Author(s):  
Kelly L. Mulligan ◽  
Terra C. Hiebert ◽  
Nicholas W. Jeffery ◽  
T. Ryan Gregory
Keyword(s):  
Flow Cytometry ◽  
Image Analysis ◽  
Body Size ◽  
Genome Size ◽  
Positive Relationship ◽  
Nuclear Dna ◽  
Nuclear Dna Content ◽  
Size Estimation ◽  
Size Diversity ◽  
Size Estimates

Ribbon worms (phylum Nemertea) are among several animal groups that have been overlooked in past studies of genome-size diversity. Here, we report genome-size estimates for eight species of nemerteans, including representatives of the major lineages in the phylum. Genome sizes in these species ranged more than fivefold, and there was some indication of a positive relationship with body size. Somatic endopolyploidy also appears to be common in these animals. Importantly, this study demonstrates that both of the most common methods of genome-size estimation (flow cytometry and Feulgen image analysis densitometry) can be used to assess genome size in ribbon worms, thereby facilitating additional efforts to investigate patterns of variability in nuclear DNA content in this phylum.

Impact of the choices of calibration points for molecular dating: a case study of Ensifera

2021 ◽  
Vol 4 (3) ◽  
Author(s):  
ANDRÉ NEL
Keyword(s):  
Molecular Dating ◽  
Rigorous Approach ◽  
Phylogenetic Studies

Fossils are crucial for molecular clade dating (Warnock et al., 2012, 2015). But it is necessary to have a rigorous approach, without rejecting taxa on poor arguments or ignoring some of them without any reasons. Here we show through two very recent examples of phylogenetic studies on the Orthoptera, that such behaviours can have dramatic consequences on the value of the results of the studies.

scholarly journals Characterization of Five New Earthworm Mitogenomes (Oligochaeta: Lumbricidae): Mitochondrial Phylogeny of Lumbricidae

Diversity ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 580
Author(s):  
Hongyi Liu ◽  
Yufeng Zhang ◽  
Wei Xu ◽  
Yu Fang ◽  
Honghua Ruan
Keyword(s):  
Phylogenetic Trees ◽  
Mitochondrial Gene ◽  
Morphological Characteristics ◽  
Molecular Techniques ◽  
Phylogenetic Studies ◽  
Octolasion Tyrtaeum ◽  
Eisenia Nordenskioldi ◽  
Novel Strategy

Identification based on conventional morphological characteristics is typically difficult and time-consuming. The development of molecular techniques provides a novel strategy that relies on specific mitochondrial gene fragments to conduct authentication. For this study, five newly sequenced partial mitogenomes of earthworms (Bimastos parvus, Dendrobaena octaedra, Eisenia andrei, Eisenia nordenskioldi, and Octolasion tyrtaeum) with lengths ranging from 14,977 to 15,715 were presented. Each mitogenome possessed a putative control region that resided between tRNA-Arg and tRNA-His. All of the PCGs were under negative selection according to the value of Ka/Ks. The phylogenetic trees supported the classification of Eisenia and Lumbricus; however, the trees based on cox1 did not. Through various comparisons, it was determined that cox1 fragments might be more suitable for molecular identification. These results lay the foundation for further phylogenetic studies on Lumbricidae.

Ploidy Variation in Fraxinus L. (Oleaceae) of Eastern North America: Genome Size Diversity and Taxonomy in a Suddenly Endangered Genus

2018 ◽  
Vol 179 (5) ◽  
pp. 377-389 ◽  
Author(s):  
Alan T. Whittemore ◽  
Julian J. N. Campbell ◽  
Zheng-Lian Xia ◽  
Craig H. Carlson ◽  
Daniel Atha ◽  
...  
Keyword(s):  
North America ◽  
Genome Size ◽  
Eastern North America ◽  
Size Diversity

An exploration of genome size diversity in dragonflies and damselflies (Insecta: Odonata)

2009 ◽  
Vol 278 (3) ◽  
pp. 163-173 ◽  
Author(s):  
A. M. Ardila‐Garcia ◽  
T. R. Gregory
Keyword(s):  
Genome Size ◽  
Size Diversity

scholarly journals Amplified Intergenic Locus Polymorphism as a Basis for Bacterial Typing of Listeria spp. and Escherichiacoli

2005 ◽  
Vol 71 (6) ◽  
pp. 3144-3152 ◽  
Author(s):  
Lilach Somer ◽  
Yael Danin-Poleg ◽  
Eran Diamant ◽  
Riva Gur-Arie ◽  
Yniv Palti ◽  
...  
Keyword(s):  
Low Cost ◽  
Size Variation ◽  
Pcr Primers ◽  
Intergenic Sequence ◽  
Bacterial Genomes ◽  
Bacterial Typing ◽  
Reading Frame ◽  
E Coli ◽  
Phylogenetic Studies ◽  
Intergenic Regions

ABSTRACT DNA-based methods are increasingly important for bacterial typing. The high number of polymorphic sites present among closely related bacterial genomes is the basis for the presented method. The method identifies multilocus genomic polymorphisms in intergenic regions termed AILP (amplified intergenic locus polymorphism). For each locus, a pair of unique PCR primers was designed to amplify an intergenic sequence from one open reading frame (ORF) to the adjacent ORF. Presence, absence, and size variation of the amplification products were identified and used as genetic markers for rapidly differentiating among strains. Polymorphism was evaluated using 18 AILP sites among 28 strains of Listeria monocytogenes and 6 strains of Listeria spp. and 30 AILP markers among 27 strains of Escherichia coli. Up to four alleles per locus were identified among Listeria strains, and up to six were identified among E. coli strains. In both species, more than half of the AILP sites revealed intraspecies polymorphism. The AILP data were applied to phylogenetic analysis among Listeria and E. coli strains. A clear distinction between L. monocytogenes and Listeria spp. was demonstrated. In addition, the method separated L. monocytogenes into the three known lineages and discriminated the most common virulent serotypic group, 4b. In E. coli, AILP analysis separated the known groups as well as the virulent O157:H7 isolates. These findings for both Listeria and E. coli are in agreement with other phylogenetic studies using molecular markers. The AILP method was found to be rapid, simple, reproducible, and a low-cost method for initial bacterial typing that could serve as a basis for epidemiological investigation.

scholarly journals Genome size diversity in orchids: consequences and evolution

2009 ◽  
Vol 104 (3) ◽  
pp. 469-481 ◽  
Author(s):  
I. J. Leitch ◽  
I. Kahandawala ◽  
J. Suda ◽  
L. Hanson ◽  
M. J. Ingrouille ◽  
...  
Keyword(s):  
Genome Size ◽  
Size Diversity

scholarly journals Tracing the evolution of the plastome and mitogenome in the Chloropicophyceae uncovered convergent tRNA gene losses and a variant plastid genetic code

2019 ◽  
Author(s):  
Monique Turmel ◽  
Adriana Lopes dos Santos ◽  
Christian Otis ◽  
Roxanne Sergerie ◽  
Claude Lemieux
Keyword(s):  
Genetic Code ◽  
Trna Gene ◽  
Marine Phytoplankton ◽  
Trna Genes ◽  
Protein Coding ◽  
Organelle Genomes ◽  
Phytoplankton Communities ◽  
Plastid Protein ◽  
Intergenic Regions ◽  
Phylogenetic Affinities

AbstractThe tiny green algae belonging to the Chloropicophyceae play a key role in marine phytoplankton communities; this newly erected class of prasinophytes comprises two genera (Chloropicon and Chloroparvula) containing each several species. We sequenced the plastomes and mitogenomes of eight Chloropicon and five Chloroparvula species to better delineate the phylogenetic affinities of these taxa and to infer the suite of changes that their organelle genomes sustained during evolution. The relationships resolved in organelle-based phylogenomic trees were essentially congruent with previously reported rRNA trees, and similar evolutionary trends but distinct dynamics were identified for the plastome and mitogenome. Although the plastome sustained considerable changes in gene content and order at the time the two genera split, subsequently it remained stable and maintained a very small size. The mitogenome, however, was remodeled more gradually and showed more fluctuation in size, mainly as a result of expansions/contractions of intergenic regions. Remarkably, the plastome and mitogenome lost a common set of three tRNA genes, with the trnI(cau) and trnL(uaa) losses being accompanied with important variations in codon usage. Unexpectedly, despite the disappearance of trnI(cau) from the plastome in the Chloroparvula lineage, AUA codons (the codons recognized by this gene product) were detected in certain plastid genes. By comparing the sequences of plastid protein-coding genes from chloropicophycean and phylogenetically diverse chlorophyte algae with those of the corresponding predicted proteins, we discovered that the AUA codon was reassigned from isoleucine to methionine in Chloroparvula. This noncanonical genetic code has not previously been uncovered in plastids.

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