scholarly journals The 256 kb mitochondrial genome of Clavaria fumosa is the largest among phylum Basidiomycota and is rich in introns and intronic ORFs

IMA Fungus ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Xu Wang ◽  
Yajie Wang ◽  
Wen Yao ◽  
Jinwen Shen ◽  
Mingyue Chen ◽  
...  
Keyword(s):  
Large Scale ◽  
Mitochondrial Gene ◽  
Mitochondrial Genes ◽  
Gene Arrangement ◽  
Repeat Sequences ◽  
Gene Sets ◽  
The Family ◽  
Intergenic Regions ◽  
Complete Mitogenome ◽  
Gain Loss

AbstractIn the present study, the complete mitogenome of Clavaria fumosa, was sequenced, assembled, and compared. The complete mitogenome of C. fumosa is 256,807 bp in length and is the largest mitogenomes among all Basidiomycota mitogenomes reported. Comparative mitogenomic analysis indicated that the C. fumosa mitogenome contained the most introns and intronic ORFs among all fungal mitogenomes. Large intergenic regions, intronic regions, accumulation of repeat sequences and plasmid-derived genes together promoted the size expansion of the C. fumosa mitogenome. In addition, the rps3 gene was found subjected to positive selection between some Agaricales species. We found frequent intron gain/loss events in Agaricales mitogenomes, and four novel intron classes were detected in the C. fumosa mitogenome. Large-scale gene rearrangements were found occurred in Agaricales species and the C. fumosa mitogenome had a unique gene arrangement which differed from other Agaricales species. Phylogenetic analysis for 76 Basidiomycetes based on combined mitochondrial gene sets indicated that mitochondrial genes could be used as effective molecular markers for reconstructing evolution of Basidiomycota. The study served as the first report on the mitogenomes of the family Clavariaceae, which will promote the understanding of the genetics, evolution and taxonomy of C. fumosa and related species.

scholarly journals Novel gene rearrangement in the mitochondrial genome of Muraenesox cinereus and the phylogenetic relationship of Anguilliformes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kun Zhang ◽  
Kehua Zhu ◽  
Yifan Liu ◽  
Hua Zhang ◽  
Li Gong ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Gene Rearrangement ◽  
Tandem Duplication ◽  
Mitochondrial Gene ◽  
Gene Arrangement ◽  
Protein Coding ◽  
Muraenesox Cinereus ◽  
Complete Mitogenome ◽  
Relationship Of ◽  
Rna Genes

AbstractThe structure and gene sequence of the fish mitochondrial genome are generally considered to be conservative. However, two types of gene arrangements are found in the mitochondrial genome of Anguilliformes. In this paper, we report a complete mitogenome of Muraenesox cinereus (Anguilliformes: Muraenesocidae) with rearrangement phenomenon. The total length of the M. cinereus mitogenome was 17,673 bp, and it contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genome of M. cinereus was obviously rearranged compared with the mitochondria of typical vertebrates. The genes ND6 and the conjoint trnE were translocated to the location between trnT and trnP, and one of the duplicated CR was translocated to the upstream of the ND6. The tandem duplication and random loss is most suitable for explaining this mitochondrial gene rearrangement. The Anguilliformes phylogenetic tree constructed based on the whole mitochondrial genome well supports Congridae non-monophyly. These results provide a basis for the future Anguilliformes mitochondrial gene arrangement characteristics and further phylogenetic research.

More limbs on the tree: mitogenome characterisation and systematic position of ‘living fossil’ species Neoglyphea inopinata and Laurentaeglyphea neocaledonica (Decapoda : Glypheidea : Glypheidae)

2018 ◽  
Vol 32 (2) ◽  
pp. 448 ◽  
Author(s):  
Mun Hua Tan ◽  
Han Ming Gan ◽  
Gavin Dally ◽  
Suzanne Horner ◽  
Paula A. Rodríguez Moreno ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Large Scale ◽  
Mitochondrial Gene ◽  
Lower Triassic ◽  
Molecular Data ◽  
Systematic Position ◽  
Fossil Species ◽  
Living Fossil ◽  
Extant Species ◽  
Complete Mitogenome

Glypheids first appeared in the Lower Triassic period and were believed to be extinct until specimens of Neoglyphea inopinata Forest & Saint Laurent and Laurentaeglyphea neocaledonica Richer de Forges were described in 1975 and 2006, respectively. The finding of extant species has meant that molecular data can now be used to complement morphological and fossil-based studies to investigate the relationships of Glypheidea within the Decapoda. However, despite several molecular studies, the placement of this infraorder within the decapod phylogenetic tree is not resolved. One limitation is that molecular resources available for glypheids have been limited to a few nuclear and mitochondrial gene fragments. Many of the more recent large-scale studies of decapod phylogeny have used information from complete mitogenomes, but have excluded the infraorder Glypheidea due to the unavailability of complete mitogenome sequences. Using next-generation sequencing, we successfully sequenced and assembled complete mitogenome sequences from museum specimens of N. inopinata and L. neocaledonica, the only two extant species of glypheids. With these sequences, we constructed the first decapod phylogenetic tree based on whole mitogenome sequences that includes Glypheidea as one of 10 decapod infraorders positioned within the suborder Pleocyemata. From this, the Glypheidea appears to be a relatively derived lineage related to the Polychelida and Astacidea. Also in our study, we conducted a survey on currently available decapod mitogenome resources available on National Center for Biotechnology Information (NCBI) and identified infraorders that would benefit from more strategic and expanded taxonomic sampling.

scholarly journals Complete Mitochondrial Genomes of Babylonia Formosae and Babylonia Zeylanica (Neogastropoda: Babyloniidae) and Increased Sampling Give New Insights Into Neogastropoda Phylogeny

2021 ◽  
Author(s):  
Hongwei Huang ◽  
huai Yang ◽  
Jiji Li ◽  
baoying Guo ◽  
Yingying Ye
Keyword(s):  
Phylogenetic Trees ◽  
Mitochondrial Gene ◽  
Gene Arrangement ◽  
Trna Genes ◽  
Phylogenetic Studies ◽  
Marine Snails ◽  
Fundamental Information ◽  
Complete Mitogenome ◽  
Genome Arrangement ◽  
Complete Mitochondrial Genomes

Abstract The phylogenetic relationships of Neogastropoda, a group of highly complex predatory marine snails, have been controversial. The two newly sequenced mitogenomes of Babylonia formosae and Babylonia zeylanica (Neogastropoda: Babyloniidae) are described. The mitogenomes of B. zeylanica and B. formosae were 16, 214 bp and 16, 181 bp in length, respectively. The mitogenomes of both species contain 13 PCGs, 22 tRNA genes, and 2 ribosomal RNA genes. The sequence of genes differed from the ancestral mitochondrial gene arrangement of Caenogastropoda mitogenomes. Also, 63 Neogastropoda species were analyzed for the genome organization of seventeen major lineage of Neogastropoda, five types of mitochondrial genome arrangement were identified. Bayesian Inference phylogenetic trees and Maximum likehood of Neogastropoda were established according to complete mitogenome. The monophyly of Neogastropoda families is strongly supported by this study, in contrast to previous molecular studies. Our results shed light on gene sequence distribution/arrangement characteristics of Neogastropoda mitogenomes, provide fundamental information for further phylogenetic studies on Neogastropoda.

scholarly journals Evolutionary Insights Into Two Widespread Ectomycorrhizal Fungi (Pisolithus) From Comparative Analysis of Mitochondrial Genomes

2021 ◽  
Vol 12 ◽  
Author(s):  
Peng Wu ◽  
Tian Yao ◽  
Yuanhang Ren ◽  
Jinghua Ye ◽  
Yuan Qing ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Positive Selection ◽  
Ectomycorrhizal Fungi ◽  
Mitochondrial Gene ◽  
Intron Loss ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Circular Dna ◽  
The Family ◽  
High Degree

The genus Pisolithus is a group of global ectomycorrhizal fungi. The characterizations of Pisolithus mitochondrial genomes have still been unknown. In the present study, the complete mitogenomes of two Pisolithus species, Pisolithus microcarpus, and Pisolithus tinctorius, were assembled and compared with other Boletales mitogenomes. Both Pisolithus mitogenomes comprised circular DNA molecules with sizes of 43,990 and 44,054 bp, respectively. Comparative mitogenomic analysis showed that the rps3 gene differentiated greatly between Boletales species, and this gene may be subjected to strong pressure of positive selection between some Boletales species. Several plasmid-derived genes and genes with unknown functions were detected in the two Pisolithus mitogenomes, which needs further analysis. The two Pisolithus species show a high degree of collinearity, which may represent the gene arrangement of the ancestors of ectomycorrhizal Boletales species. Frequent intron loss/gain events were detected in Boletales and basidiomycetes, and intron P717 was only detected in P. tinctorius out of the eight Boletales mitogenomes tested. We reconstructed phylogeny of 79 basidiomycetes based on combined mitochondrial gene dataset, and obtained well-supported phylogenetic topologies. This study served as the first report on the mitogenomes of the family Pisolithaceae, which will promote the understanding of the evolution of Pisolithus species.

scholarly journals Molecular phylogeny of Toxoplasmatinae: comparison between inferences based on mitochondrial and apicoplast genetic sequences

2016 ◽  
Vol 25 (1) ◽  
pp. 82-89 ◽  
Author(s):  
Michelle Klein Sercundes ◽  
Samantha Yuri Oshiro Branco Valadas ◽  
Lara Borges Keid ◽  
Tricia Maria Ferreira Souza Oliveira ◽  
Helena Lage Ferreira ◽  
...  
Keyword(s):  
Neospora Caninum ◽  
Mitochondrial Gene ◽  
Mitochondrial Genes ◽  
Sarcocystis Neurona ◽  
Gene Coding ◽  
The Family ◽  
Caseinolytic Protease ◽  
Evolutionary Studies ◽  
Genetic Sequences ◽  
Sarcocystis Falcatula

Abstract Phylogenies within Toxoplasmatinae have been widely investigated with different molecular markers. Here, we studied molecular phylogenies of the Toxoplasmatinae subfamily based on apicoplast and mitochondrial genes. Partial sequences of apicoplast genes coding for caseinolytic protease (clpC) and beta subunit of RNA polymerase (rpoB), and mitochondrial gene coding for cytochrome B (cytB) were analyzed. Laboratory-adapted strains of the closely related parasites Sarcocystis falcatula and Sarcocystis neurona were investigated, along with Neospora caninum, Neospora hughesi, Toxoplasma gondii (strains RH, CTG and PTG), Besnoitia akodoni, Hammondia hammondiand two genetically divergent lineages of Hammondia heydorni. The molecular analysis based on organellar genes did not clearly differentiate between N. caninum and N. hughesi, but the two lineages of H. heydorni were confirmed. Slight differences between the strains of S. falcatula and S. neurona were encountered in all markers. In conclusion, congruent phylogenies were inferred from the three different genes and they might be used for screening undescribed sarcocystid parasites in order to ascertain their phylogenetic relationships with organisms of the family Sarcocystidae. The evolutionary studies based on organelar genes confirm that the genusHammondia is paraphyletic. The primers used for amplification of clpC and rpoB were able to amplify genetic sequences of organisms of the genus Sarcocystisand organisms of the subfamily Toxoplasmatinae as well.

A Family With Autosomal-Dominant Progressive Sensorineural Hearing Loss

1996 ◽  
Vol 5 (1) ◽  
pp. 23-32 ◽  
Author(s):  
Chris Halpin ◽  
Barbara Herrmann ◽  
Margaret Whearty
Keyword(s):  
Speech Production ◽  
Hearing Aids ◽  
Role Models ◽  
Speech Intelligibility ◽  
Large Scale ◽  
Speech Language Pathology ◽  
The Family ◽  
Patient Will ◽  
Language Pathology

The family described in this article provides an unusual opportunity to relate findings from genetic, histological, electrophysiological, psychophysical, and rehabilitative investigation. Although the total number evaluated is large (49), the known, living affected population is smaller (14), and these are spread from age 20 to age 59. As a result, the findings described above are those of a large-scale case study. Clearly, more data will be available through longitudinal study of the individuals documented in the course of this investigation but, given the slow nature of the progression in this disease, such studies will be undertaken after an interval of several years. The general picture presented to the audiologist who must rehabilitate these cases is that of a progressive cochlear degeneration that affects only thresholds at first, and then rapidly diminishes speech intelligibility. The expected result is that, after normal language development, the patient may accept hearing aids well, encouraged by the support of the family. Performance and satisfaction with the hearing aids is good, until the onset of the speech intelligibility loss, at which time the patient will encounter serious difficulties and may reject hearing aids as unhelpful. As the histological and electrophysiological results indicate, however, the eighth nerve remains viable, especially in the younger affected members, and success with cochlear implantation may be expected. Audiologic counseling efforts are aided by the presence of role models and support from the other affected members of the family. Speech-language pathology services were not considered important by the members of this family since their speech production developed normally and has remained very good. Self-correction of speech was supported by hearing aids and cochlear implants (Case 5’s speech production was documented in Perkell, Lane, Svirsky, & Webster, 1992). These patients received genetic counseling and, due to the high penetrance of the disease, exhibited serious concerns regarding future generations and the hope of a cure.

The Use of Medical Record Linkage for Population and Genetic Studies

1969 ◽  
Vol 08 (01) ◽  
pp. 07-11 ◽  
Author(s):  
H. B. Newcombe
Keyword(s):  
Record Linkage ◽  
Large Scale ◽  
Medical Record Linkage ◽  
Canadian Province ◽  
Genetic Studies ◽  
Parental Characteristics ◽  
Family Histories ◽  
The Family ◽  
Large Populations ◽  
Machine Readable

Methods are described for deriving personal and family histories of birth, marriage, procreation, ill health and death, for large populations, from existing civil registrations of vital events and the routine records of ill health. Computers have been used to group together and »link« the separately derived records pertaining to successive events in the lives of the same individuals and families, rapidly and on a large scale. Most of the records employed are already available as machine readable punchcards and magnetic tapes, for statistical and administrative purposes, and only minor modifications have been made to the manner in which these are produced.As applied to the population of the Canadian province of British Columbia (currently about 2 million people) these methods have already yielded substantial information on the risks of disease: a) in the population, b) in relation to various parental characteristics, and c) as correlated with previous occurrences in the family histories.

scholarly journals Mitochondrial Genomes from Two Specialized Subfamilies of Reduviidae (Insecta: Hemiptera) Reveal Novel Gene Rearrangements of True Bugs

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1134
Author(s):  
Fei Ye ◽  
Hu Li ◽  
Qiang Xie
Keyword(s):  
Gene Rearrangement ◽  
Hot Spot ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Deep Understanding ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Current View ◽  
Novel Gene ◽  
Spot Group

Reduviidae, a hyper-diverse family, comprise 25 subfamilies with nearly 7000 species and include many natural enemies of crop pests and vectors of human disease. To date, 75 mitochondrial genomes (mitogenomes) of assassin bugs from only 11 subfamilies have been reported. The limited sampling of mitogenome at higher categories hinders a deep understanding of mitogenome evolution and reduviid phylogeny. In this study, the first mitogenomes of Holoptilinae (Ptilocnemus lemur) and Emesinae (Ischnobaenella hainana) were sequenced. Two novel gene orders were detected in the newly sequenced mitogenomes. Combined 421 heteropteran mitogenomes, we identified 21 different gene orders and six gene rearrangement units located in three gene blocks. Comparative analyses of the diversity of gene order for each unit reveal that the tRNA gene cluster trnI-trnQ-trnM is the hotspot of heteropteran gene rearrangement. Furthermore, combined analyses of the gene rearrangement richness of each unit and the whole mitogenome among heteropteran lineages confirm Reduviidae as a ‘hot-spot group’ of gene rearrangement in Heteroptera. The phylogenetic analyses corroborate the current view of phylogenetic relationships between basal groups of Reduviidae with high support values. Our study provides deeper insights into the evolution of mitochondrial gene arrangement in Heteroptera and the early divergence of reduviids.

scholarly journals Sinonasal FUS-ERG-Rearranged Ewing’s Sarcoma Mimicking Glomangiopericytoma

2020 ◽  
Vol 13 (3) ◽  
pp. 1393-1396
Author(s):  
Maggie Zhou ◽  
Yen Chen Kevin Ko ◽  
Gregory W. Charville ◽  
Kristen N. Ganjoo
Keyword(s):  
Ewing’S Sarcoma ◽  
Ewing's Sarcoma ◽  
Staining Pattern ◽  
Gene Arrangement ◽  
Round Cell ◽  
The Family ◽  
History Of ◽  
Blue Cell ◽  
Aggressive Tumor ◽  
Membranous Staining

Ewing’s sarcoma is a rare and aggressive tumor that typically arises in the long bones of the extremities. It belongs in the family of small round blue cell tumors and is characterized immunohistochemically by diffuse CD99 expression and molecularly by one of several oncogenic translocations, most commonly t(11;22)(q24;q12) between the <i>EWSR1</i> gene and the <i>FLI1</i> gene. Here we present a rare case of Ewing’s sarcoma in the sinonasal tract with <i>FUS-ERG</i> gene arrangement that was regarded for almost a decade as a sinonasal-type hemangiopericytoma (glomangiopericytoma). This case illustrates the surprisingly prolonged natural history of Ewing’s sarcoma that did not receive therapy for many years and the importance of considering alternative genetic translocations. Our experience suggests that the presence of diffuse CD99 membranous staining pattern in a small blue round cell tumor with morphology typical for Ewing’s sarcoma but FISH negative for <i>EWSR1</i> rearrangement should prompt consideration of <i>FUS-ERG</i> fusion.

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