scholarly journals Mitochondrial genomes of two Polydora (Spionidae) species provide further evidence that mitochondrial architecture in the Sedentaria (Annelida) is not conserved

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lingtong Ye ◽  
Tuo Yao ◽  
Jie Lu ◽  
Jingzhe Jiang ◽  
Changming Bai
Keyword(s):  
Purifying Selection ◽  
Economic Losses ◽  
Mitochondrial Genomes ◽  
Selection Pressures ◽  
Marine Mollusk ◽  
Coding Regions ◽  
The Third ◽  
Large Size ◽  
Early Evidence ◽  
Architecture Evolution

AbstractContrary to the early evidence, which indicated that the mitochondrial architecture in one of the two major annelida clades, Sedentaria, is relatively conserved, a handful of relatively recent studies found evidence that some species exhibit elevated rates of mitochondrial architecture evolution. We sequenced complete mitogenomes belonging to two congeneric shell-boring Spionidae species that cause considerable economic losses in the commercial marine mollusk aquaculture: Polydora brevipalpa and Polydora websteri. The two mitogenomes exhibited very similar architecture. In comparison to other sedentarians, they exhibited some standard features, including all genes encoded on the same strand, uncommon but not unique duplicated trnM gene, as well as a number of unique features. Their comparatively large size (17,673 bp) can be attributed to four non-coding regions larger than 500 bp. We identified an unusually large (putative) overlap of 14 bases between nad2 and cox1 genes in both species. Importantly, the two species exhibited completely rearranged gene orders in comparison to all other available mitogenomes. Along with Serpulidae and Sabellidae, Polydora is the third identified sedentarian lineage that exhibits disproportionally elevated rates of mitogenomic architecture rearrangements. Selection analyses indicate that these three lineages also exhibited relaxed purifying selection pressures.

scholarly journals One Hundred Mitochondrial Genomes of Cicadas

2018 ◽  
Vol 110 (2) ◽  
pp. 247-256 ◽  
Author(s):  
Piotr Łukasik ◽  
Rebecca A Chong ◽  
Katherine Nazario ◽  
Yu Matsuura ◽  
De Anna C Bublitz ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Purifying Selection ◽  
Evolutionary Rates ◽  
Future Research ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Coding Regions ◽  
Mitochondrial Genome Evolution ◽  
Taxonomic Framework

Abstract Mitochondrial genomes can provide valuable information on the biology and evolutionary histories of their host organisms. Here, we present and characterize the complete coding regions of 107 mitochondrial genomes (mitogenomes) of cicadas (Insecta: Hemiptera: Auchenorrhyncha: Cicadoidea), representing 31 genera, 61 species, and 83 populations. We show that all cicada mitogenomes retain the organization and gene contents thought to be ancestral in insects, with some variability among cicada clades in the length of a region between the genes nad2 and cox1, which encodes 3 tRNAs. Phylogenetic analyses using these mitogenomes recapitulate a recent 5-gene classification of cicadas into families and subfamilies, but also identify a species that falls outside of the established taxonomic framework. While protein-coding genes are under strong purifying selection, tests of relative evolutionary rates reveal significant variation in evolutionary rates across taxa, highlighting the dynamic nature of mitochondrial genome evolution in cicadas. These data will serve as a useful reference for future research into the systematics, ecology, and evolution of the superfamily Cicadoidea.

scholarly journals A Cluster of Cuticle Protein Genes of Drosophila melanogaster at 65A: Sequence, Structure and Evolution

Genetics ◽  
1997 ◽  
Vol 147 (3) ◽  
pp. 1213-1224
Author(s):  
Jean-Philippe Charles ◽  
Carol Chihara ◽  
Shamim Nejad ◽  
Lynn M Riddiford
Keyword(s):  
Drosophila Melanogaster ◽  
Genomic Dna ◽  
Multiple Copy ◽  
Sequence Structure ◽  
Coding Regions ◽  
The Third ◽  
Genetic Complexity ◽  
Genes Encoding ◽  
Cuticle Protein ◽  
Cuticle Proteins

A 36-kb genomic DNA segment of the Drosophila melanogaster genome containing 12 clustered cuticle genes has been mapped and partially sequenced. The cluster maps at 65A 5-6 on the left arm of the third chromosome, in agreement with the previously determined location of a putative cluster encompassing the genes for the third instar larval cuticle proteins LCP5, LCP6 and LCP8. This cluster is the largest cuticle gene cluster discovered to date and shows a number of surprising features that explain in part the genetic complexity of the LCP5, LCP6 and LCP8 loci. The genes encoding LCP5 and LCP8 are multiple copy genes and the presence of extensive similarity in their coding regions gives the first evidence for gene conversion in cuticle genes. In addition, five genes in the cluster are intronless. Four of these five have arisen by retroposition. The other genes in the cluster have a single intron located at an unusual location for insect cuticle genes.

scholarly journals Not Frozen in the Ice: large and Dynamic Rearrangements in the Mitochondrial Genomes of the Antarctic Fish

2021 ◽  
Author(s):  
Chiara Papetti ◽  
Massimiliano Babbucci ◽  
Agnes Dettai ◽  
Andrea Basso ◽  
Magnus Lucassen ◽  
...  
Keyword(s):  
Gene Order ◽  
Hot Spot ◽  
Mitochondrial Gene ◽  
Antarctic Fish ◽  
Purifying Selection ◽  
Compositional Bias ◽  
Mitochondrial Genomes ◽  
Notothenioid Fish ◽  
Antarctic Notothenioids ◽  
The Antarctic

Abstract The vertebrate mitochondrial genomes generally present a typical gene order. Exceptions are uncommon and important to study the genetic mechanisms of gene order rearrangements and their consequences on phylogenetic output and mitochondrial function. Antarctic notothenioid fish carry some peculiar rearrangements of the mitochondrial gene order. In this first systematic study of 28 species, we analysed known and undescribed mitochondrial genome rearrangements for a total of eight different gene orders within the notothenioid fish. Our reconstructions suggest that transpositions, duplications and inversion of multiple genes are the most likely mechanisms of rearrangement in notothenioid mitochondrial genomes. In Trematominae, we documented an extremely rare inversion of a large genomic segment of 5300 bp that partially affected the gene compositional bias but not the phylogenetic output. The genomic region delimited by nad5 and trnF, close to the area of the Control Region, was identified as the hot spot of variation in Antarctic fish mitochondrial genomes. Analysing the sequence of several intergenic spacers and mapping the arrangements on a newly generated phylogeny showed that the entire history of the Antarctic notothenioids is characterized by multiple, relatively rapid, events of disruption of the gene order. We hypothesised that a pre-existing genomic flexibility of the ancestor of the Antarctic notothenioids may have generated a precondition for gene order rearrangement, and the pressure of purifying selection could have worked for a rapid restoration of the mitochondrial functionality and compactness after each event of rearrangement.

scholarly journals Jaws of a large belemnite and an ammonite from the Aalenian (Middle Jurassic) of Switzerland

2020 ◽  
Vol 139 (1) ◽  
Author(s):  
Christian Klug ◽  
Walter Etter ◽  
René Hoffmann ◽  
Dirk Fuchs ◽  
Kenneth De Baets
Keyword(s):  
Middle Jurassic ◽  
Opalinus Clay ◽  
Northern Switzerland ◽  
The Third ◽  
Large Size ◽  
Upper Jaw ◽  
Rule Out

AbstractAlthough belemnite rostra can be quite abundant in Jurassic and Cretaceous strata, the record of belemnite jaws was limited to a few specimens from Germany and Russia. Here, we describe and figure three cephalopod jaws from the Middle Jurassic Opalinus Clay of northern Switzerland. Although flattened, the carbonaceous fossils display enough morphological information to rule out an ammonoid, nautiloid or octobrachian origin of the two larger jaws. Their similarities to belemnite jaws from Germany and Russia conforms with our interpretation of these specimens as belemnite jaws. Based on their rather large size, we tentatively assign these two jaws to the megateuthidid Acrocoelites conoideus. The third jaw is a rather small upper jaw of an ammonoid. Since Leioceras opalinum is by far the most common ammonite in this unit in northern Switzerland, we tentatively suggest that the upper jaw belongs to this species.

scholarly journals A ‘Giant Microfossil’ from the Gunflint Chert and its Implications for Fungal and Eukaryote Origins

2019 ◽  
Author(s):  
Mark A. S. McMenamin ◽  
Aurora Curtis-Hill ◽  
Sophie Rabinow ◽  
Kalyndi Martin ◽  
Destiny Treloar
Keyword(s):  
Thin Section ◽  
Asexual Reproduction ◽  
Alternaria Alternata ◽  
Fossil Record ◽  
Iron Formation ◽  
Southern Ontario ◽  
Large Size ◽  
Early Evidence

We report here a giant microfossil resembling the conidium of an ascomycete fungus (cf. Alternaria alternata). The specimen is preserved in stromatolitic black chert of the Gunflint Iron Formation (Paleoproterozoic Eon, Orosirian Period, ca. 1.9-2.0 Ga) of southern Ontario, Canada, and the rock that provided the thin section may have been collected by Elso Barghoorn as part of the original discovery of the Gunflint microbiota. The large size of the fossil sets it apart from other, tiny by comparison, Gunflint microfossils. The fossil is 200 microns in length and has cross walls. Individual cells are 30-46 microns in greatest dimension. The apical ‘spore’ is cap-shaped, and has partly separated from the rest of the structure. Cloulicaria gunflintensis gen. nov. sp. nov. may provide early evidence for eukaryotes (fungi) in the fossil record, and may also represent the earliest evidence for asexual reproduction in a eukaryote by means of mitospores.

scholarly journals A ‘Giant Microfossil’ from the Gunflint Chert and its Implications for Eukaryote Origins

2019 ◽  
Author(s):  
Mark McMenamin
Keyword(s):  
Thin Section ◽  
Asexual Reproduction ◽  
Alternaria Alternata ◽  
Fossil Record ◽  
Iron Formation ◽  
Southern Ontario ◽  
Large Size ◽  
Early Evidence

We report here a ‘giant microfossil’ resembling the conidium of an ascomycete fungus (cf. Alternaria alternata). The specimen is preserved in stromatolitic black chert of the Gunflint Iron Formation (Paleoproterozoic Eon, Orosirian Period, ca. 1.9-2.0 Ga) of southern Ontario, Canada, and the rock that provided the thin section may have been collected by Elso Barghoorn as part of the original discovery of the Gunflint microbiota. The large size of the fossil sets it apart from other, tiny by comparison, Gunflint microfossils. The fossil is 200 microns in length and has cross walls. Individual cells are 30-46 microns in greatest dimension. The apical ‘spore’ is cap-shaped, and has partly separated from the rest of the structure. Cloulicaria gunflintensis gen. nov. sp. nov. may provide early evidence for eukaryotes (fungi) in the fossil record, and may also represent the earliest evidence for asexual reproduction in a eukaryote by means of mitospores.

scholarly journals Eusociality Shapes Convergent Patterns of Molecular Evolution across Mitochondrial Genomes of Snapping Shrimps

2020 ◽  
Author(s):  
Solomon T C Chak ◽  
Juan Antonio Baeza ◽  
Phillip Barden
Keyword(s):  
Molecular Evolution ◽  
Genome Evolution ◽  
Purifying Selection ◽  
Synonymous Substitution ◽  
Mitochondrial Genomes ◽  
Comparative Genomic ◽  
Effective Population ◽  
Protein Coding ◽  
Marine Realm ◽  
Snapping Shrimps

Abstract Eusociality is a highly conspicuous and ecologically impactful behavioral syndrome that has evolved independently across multiple animal lineages. So far, comparative genomic analyses of advanced sociality have been mostly limited to insects. Here, we study the only clade of animals known to exhibit eusociality in the marine realm—lineages of socially diverse snapping shrimps in the genus Synalpheus. To investigate the molecular impact of sociality, we assembled the mitochondrial genomes of eight Synalpheus species that represent three independent origins of eusociality and analyzed patterns of molecular evolution in protein-coding genes. Synonymous substitution rates are lower and potential signals of relaxed purifying selection are higher in eusocial relative to noneusocial taxa. Our results suggest that mitochondrial genome evolution was shaped by eusociality-linked traits—extended generation times and reduced effective population sizes that are hallmarks of advanced animal societies. This is the first direct evidence of eusociality impacting genome evolution in marine taxa. Our results also strongly support the idea that eusociality can shape genome evolution through profound changes in life history and demography.

scholarly journals Glyptogidiella omanica gen. et sp. nov., an inland groundwater bogidiellid from Oman with enlarged coxal plate V (Crustacea, Amphipoda)

Zootaxa ◽  
2010 ◽  
Vol 2657 (1) ◽  
pp. 55 ◽  
Author(s):  
RONALD VONK ◽  
DAMIÀ JAUME
Keyword(s):  
New Genus ◽  
Sultanate Of Oman ◽  
New Genus And Species ◽  
The Third ◽  
Ground Waters ◽  
Large Size ◽  
The Family ◽  
Primary Habitat ◽  
Combined Display

A new genus and species of Amphipoda is reported from inland ground waters of the Sultanate of Oman. Although Glyptogidiella omanica gen. et sp. nov. exhibits several features typical of the Bogidiellidae (i. e. combined display of distinct carpal lobe on first gnathopod, reduced pleopodal rami, and unsegmented exopodite of third uropod), its exceptionally large fifth coxal plate and short rami of third uropod do not fit in the restricted diagnosis of the family as recently presented elsewhere. In fact, the enlarged coxal plate V is a feature not reported in any other amphipod, whereas no other bogidiellid displays an expanded basis on pereopod VII. The habitus of Glyptogidiella is not typical for a dweller of a true interstitial niche, with its short antennae, large coxal plate and short and stubby rami on the third uropod. This suggests that the interstitial medium could not be the primary habitat for the species, and that the underground of wadis might contain interstices of large size and could also be in contact with karstic hollows.

scholarly journals III. Contributions to the anatomy of the central nervous system in vertebrated animals. Part I.—Ichthyopsida. Section I.—Pisces. Subsection III.—Dipnoi. On the brain of the Ceratodus forsteri

1888 ◽  
Vol 43 (258-265) ◽  
pp. 420-423
Keyword(s):  
Fourth Ventricle ◽  
Third Ventricle ◽  
Pia Mater ◽  
The Third ◽  
Lateral Ventricles ◽  
Large Size ◽  
General Arrangement ◽  
Tela Choroidea ◽  
The Central Nervous System ◽  
The Brain

The brain of Ceratodus has the following general arrangement:—The membrane which represents the pia mater is of great thickness and toughness; there are two regions where a tela choroidea is developed: one where it covers in the fourth ventricle, and the other where it penetrates through the third ventricle and separates the lateral ventricles from each other. The ventricles are all of large size, and the walls of the lateral ventricles are not completed by nervous tissue. The thalamence-phalon and the mesencephalon are narrow, and the medulla oblongata is wide.

scholarly journals Comparative Analysis of Complete Mitochondrial Genomes of Three Gerres Fishes (Perciformes: Gerreidae) and Primary Exploration of Their Evolution History

2020 ◽  
Vol 21 (5) ◽  
pp. 1874 ◽  
Author(s):  
Huiting Ruan ◽  
Min Li ◽  
Zhenhai Li ◽  
Jiajie Huang ◽  
Weiyuan Chen ◽  
...  
Keyword(s):  
Purifying Selection ◽  
Living Environment ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Marine Fishery ◽  
Gc Skew ◽  
The Difference ◽  
Early Paleogene ◽  
Complete Mitochondrial Genomes

Mitochondrial genome is a powerful molecule marker to explore phylogenetic relationships and reveal molecular evolution in ichthyological studies. Gerres species play significant roles in marine fishery, but its evolution has received little attention. To date, only two Gerres mitochondrial genomes were reported. In the present study, three mitogenomes of Gerres (Gerres filamentosus, Gerres erythrourus, and Gerres decacanthus) were systemically investigated. The lengths of the mitogenome sequences were 16,673, 16,728, and 16,871 bp for G. filamentosus, G. erythrourus, and G. decacanthus, respectively. Most protein-coding genes (PCGs) were initiated with the typical ATG codon and terminated with the TAA codon, and the incomplete termination codon T/TA could be detected in the three species. The majority of AT-skew and GC-skew values of the 13 PCGs among the three species were negative, and the amplitude of the GC-skew was larger than the AT-skew. The genetic distance and Ka/Ks ratio analyses indicated 13 PCGs were suffering purifying selection and the selection pressures were different from certain deep-sea fishes, were which most likely due to the difference in their living environment. The phylogenetic tree was constructed by molecular method (Bayesian Inference (BI) and maximum Likelihood (ML)), providing further supplement to the scientific classification of fish. Three Gerres species were differentiated in late Cretaceous and early Paleogene, and their evolution might link with the geological events that could change their survival environment.

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