The mitochondrial genome of Ruspolia dubia (Orthoptera: Conocephalidae) contains a short A+T-rich region of 70 bp in length

Genome ◽  
2007 ◽  
Vol 50 (9) ◽  
pp. 855-866 ◽  
Author(s):  
Zhijun Zhou ◽  
Yuan Huang ◽  
Fuming Shi
Keyword(s):  
Mitochondrial Genome ◽  
Codon Usage ◽  
Base Composition ◽  
Large Subunit ◽  
Secondary Structures ◽  
Small Subunit ◽  
Complete Sequence ◽  
Mitochondrial Genomes ◽  
Rich Region ◽  
Large Subunit Rrna

The complete sequence (14 971 bp) of the Ruspolia dubia mitochondrial genome was determined and annotated. The genome contains the gene content, base composition, and codon usage typical of metazoan mitochondrial genomes. All 37 genes are conserved in the positions observed most frequently in insect mitochondrial genome structures. The secondary structures of both small subunit and large subunit rRNA were predicted. The most unusual features found were the initiation codon (TTA) of COI and a short A+T-rich region of 70 bp in length. In addition, a short, highly conserved polythymidine stretch that was previously described in Orthoptera and Diptera was also present in the A+T-rich region.

scholarly journals Complete mitochondrial genome of Glomeridesmus spelaeus (Diplopoda), a troglobitic species from Carajás iron-ore caves (Pará, Brazil)

2017 ◽  
Author(s):  
Gisele Lopes Nunes ◽  
Renato Renison Moreira Oliveira ◽  
Eder Soares Pires ◽  
Santelmo Vasconcelos ◽  
Thadeu Pietrobon ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Base Composition ◽  
Iron Ore ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Significant Advance ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Rich Region ◽  
The Public

AbstractWe report the complete mitochondrial genome sequence of Glomeridesmus spelaeus, the first sequenced genome of the order Gomeridesmida. The genome is 14,825 pb in length and encodes 37 mitochondrial (13 PCGs, 2 rRNA genes, 22 tRNA) genes and contains a typical AT-rich region. The base composition of the genome was A (40.1%), T (36.4%), C (15.8%), and G (7.6%), with an AT content of 76.5%. Our results indicated that Glomeridesmus spelaeus only distantly related to the other Diplopoda species with available mitochondrial genomes in the public databases. The publication of the mitogenome of G. spelaeus will contribute to the identification of troglobitic invertebrates, a very significant advance for the conservation of the troglofauna.

scholarly journals Pre-AIDS Era Isolates of Pneumocystis carinii f. sp. hominis: High Genotypic Similarity with Contemporary Isolates

1998 ◽  
Vol 36 (1) ◽  
pp. 90-93 ◽  
Author(s):  
Anthony G. Tsolaki ◽  
Pieter Beckers ◽  
Ann E. Wakefield
Keyword(s):  
Large Subunit ◽  
Pneumocystis Carinii ◽  
Small Subunit ◽  
Its Sequence ◽  
Small Subunit Rrna ◽  
Aids Pandemic ◽  
Genes Encoding ◽  
Lsu Rrna ◽  
Large Subunit Rrna ◽  
Sequence Types

Isolates of Pneumocystis carinii f. sp.hominis were examined from six individuals who died ofP. carinii pneumonia between 1968 and 1981 and who had underlying immunodeficiencies which were not due to human immunodeficiency virus infection. DNA sequence variation was analyzed in the genes encoding the mitochondrial large subunit rRNA (mt LSU rRNA), the internal transcribed spacer (ITS) regions of the nuclear rRNA, the arom locus, and the mitochondrial small subunit rRNA. No major variations were observed when these isolates were compared to isolates from HIV-infected individuals. A small number of minor differences were detected. A new position at which variation occurred in the mt LSU rRNA was observed in one sample. Three new ITS sequence types were identified. A total of nine different ITS sequence types were found in the six samples. Mixed infection with different ITS sequence types of P. carinii f. sp. hominis was observed in four of the six samples. The ITS locus was the most informative of the four loci for distinguishing among the isolates ofP. carinii f. sp. hominis. The data suggest that isolates of P. carinii f. sp. hominis from before the AIDS pandemic are genetically very similar to those currently found in HIV-infected individuals.

scholarly journals Three Small Nucleolar RNAs Identified from the Spliced Leader-Associated RNA Locus in Kinetoplastid Protozoans

1998 ◽  
Vol 18 (8) ◽  
pp. 4409-4417 ◽  
Author(s):  
T. Guy Roberts ◽  
Nancy R. Sturm ◽  
Billy K. Yee ◽  
Michael C. Yu ◽  
Toinette Hartshorne ◽  
...  
Keyword(s):  
Large Subunit ◽  
Small Subunit ◽  
Cell Fractionation ◽  
Small Nucleolar Rnas ◽  
Small Subunit Rrna ◽  
Base Pairs ◽  
Spliced Leader ◽  
Repeat Units ◽  
Large Subunit Rrna ◽  
Nucleolar Rnas

ABSTRACT First characterized in Trypanosoma brucei, the spliced leader-associated (SLA) RNA gene locus has now been isolated from the kinetoplastids Leishmania tarentolae and Trypanosoma cruzi. In addition to the T. brucei SLA RNA, bothL. tarentolae and T. cruzi SLA RNA repeat units also yield RNAs of 75 or 76 nucleotides (nt), 92 or 94 nt, and ∼450 or ∼350 nt, respectively, each with significant sequence identity to transcripts previously described from the T. brucei SLA RNA locus. Cell fractionation studies localize the three additional RNAs to the nucleolus; the presence of box C/D-like elements in two of the transcripts suggests that they are members of a class of small nucleolar RNAs (snoRNAs) that guide modification and cleavage of rRNAs. Candidate rRNA-snoRNA interactions can be found for one domain in each of the C/D element-containing RNAs. The putative target site for the 75/76-nt RNA is a highly conserved portion of the small subunit rRNA that contains 2′-O-ribose methylation at a conserved position (Gm1830) in L. tarentolae and in vertebrates. The 92/94-nt RNA has the potential to form base pairs near a conserved methylation site in the large subunit rRNA, which corresponds to position Gm4141 of small rRNA 2 in T. brucei. These data suggest that trypanosomatids do not obey the general 5-bp rule for snoRNA-mediated methylation.

Schistonchus hirtus n. sp. (Nematoda: Aphelenchoididae), an associate of Ficus hirta in China

Nematology ◽  
2010 ◽  
Vol 12 (4) ◽  
pp. 543-556 ◽  
Author(s):  
Yongsan Zeng ◽  
Weimin Ye ◽  
Robin M. Giblin-Davis ◽  
Changhui Li ◽  
Zhijian Du ◽  
...  
Keyword(s):  
Sequence Data ◽  
Large Subunit ◽  
Morphological Characters ◽  
Small Subunit ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Wasp Species ◽  
Dna Sequence Data ◽  
Ficus Hirta ◽  
Large Subunit Rrna

Abstract A nematode recovered from syconia of Ficus hirta from Guangzhou, P. R. China, during a survey of nematode biodiversity from 2007 to 2009, is described herein as Schistonchus hirtus n. sp. and is differentiated by a combination of morphological characters, including excretory pore (EP) located near the metacorpus, a short post-uterine sac (PUS) (0.5 vulval body diam. (VBD) long), rose thorn-shaped spicules, amoeboid sperm, absence of gubernaculum, three pairs of subventral papillae on the male tail, host-Ficus and host-wasp species and DNA sequence data. Morphologically, S. hirtus n. sp. is close to S. centerae, S. altermacrophylla, S. aureus, S. laevigatus and S. virens based upon the length of the PUS (about 0.5 VBD long). However, the relative position of the EP in S. hirtus n. sp. is very different from these species (near metacorpus vs near head). With regard to the EP character, S. hirtus n. sp. is very similar to S. macrophylla, S. guangzhouensis and S. caprifici where the EP is at metacorpus level. However, S. hirtus n. sp. differs from S. macrophylla and S. guangzhouensis by possessing a shorter PUS and smaller spicules, and differs from S. caprifici by a shorter female stylet and smaller spicules. Schistonchus hirtus n. sp. was easily differentiated from other sequenced species by the proportion of parsimony informative changes in the partial small subunit rRNA gene (SSU) and D2/D3 expansion segments of the large subunit rRNA gene (LSU). Phylogenetic analysis with SSU sequences suggests that S. hirtus n. sp. is in a highly supported monophyletic clade with Aphelenchoides and Laimaphelenchus and is polyphyletic to other sequenced Schistonchus species. With LSU sequence data, it forms a clade with S. caprifici and they appear polyphyletic relative to S. guangzhouensis, S. centerae, S. aureus, S. laevigatus and S. virens.

scholarly journals Organization and phylogenetic relationships of the mitochondrial genomes of Speiredonia retorta and other lepidopteran insects

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yu Sun ◽  
Hua Huang ◽  
Yudong Liu ◽  
Shanshan Liu ◽  
Jun Xia ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Genomes ◽  
Base Pairs ◽  
Rich Region ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Lepidopteran Insects

AbstractIn this study, we analyzed the complete mitochondrial genome (mitogenome) of Speiredonia retorta, which is a pest and a member of the Lepidoptera order. In total, the S. retorta mitogenome was found to contain 15,652 base pairs encoding 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, as well as an adenine (A) + thymine (T)-rich region. These findings were consistent with the mitogenome composition of other lepidopterans, as we identified all 13 PCGs beginning at ATN codons. We also found that 11 PCGs terminated with canonical stop codons, whereas cox2 and nad4 exhibited incomplete termination codons. By analyzing the mitogenome of S. retorta using Bayesian inference (BI) and maximum likelihood (ML) models, we were able to further confirm that this species is a member of the Erebidae family.

scholarly journals The mitochondrial genomes of the mesozoans Intoshia linei, Dicyema sp., and Dicyema japonicum

2018 ◽  
Author(s):  
Helen. E. Robertson ◽  
Philipp. H. Schiffer ◽  
Maximilian. J. Telford
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Protein ◽  
Small Subunit ◽  
Mitochondrial Genomes ◽  
List Type ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Cell Layers

AbstractThe Dicyemida and Orthonectida are two groups of tiny, simple, vermiform parasites that have historically been united in a group named the Mesozoa. Both Dicyemida and Orthonectida have just two cell layers and appear to lack any defined tissues. They were initially thought to be evolutionary intermediates between protozoans and metazoans but more recent analyses indicate that they are protostomian metazoans that have undergone secondary simplification from a complex ancestor. Here we describe the first almost complete mitochondrial genome sequence from an orthonectid, Intoshia linei, and describe nine and eight mitochondrial protein-coding genes from Dicyema sp. and Dicyema japonicum, respectively. The 14,247 base pair long I. linei sequence has typical metazoan gene content, but is exceptionally AT-rich, and has a divergent gene order compared to other metazoans. The data we present from the Dicyemida provide very limited support for the suggestion that dicyemid mitochondrial genes are found on discrete mini-circles, as opposed to the large circular mitochondrial genomes that are typical across the Metazoa. The cox1 gene from dicyemid species has a series of conserved in-frame deletions that is unique to this lineage. Using cox1 genes from across the genus Dicyema, we report the first internal phylogeny of this group.Key FindingsWe report the first almost-complete mitochondrial genome from an orthonectid parasite, Intoshia linei, including 12 protein-coding genes; 20 tRNAs and putative sequences for large and small subunit rRNAs. We find that the I. linei mitochondrial genome is exceptionally AT-rich and has a novel gene order compared to other published metazoan mitochondrial genomes. These findings are indicative of the rapid rate of evolution that has occurred in the I. linei mitochondrial genome.We also report nine and eight protein-coding genes, respectively, from the dicyemid species Dicyema sp. and Dicyema japonicum, and use the cox1 genes from both species for phylogenetic inference of the internal phylogeny of the dicyemids.We find that the cox1 gene from dicyemids has a series of four conserved in-frame deletions which appear to be unique to this group.

Dothidea kunmingensis, a novel asexual species of Dothideaceae on Jasminum nudiflorum (winter jasmine) from Southwestern China

Phytotaxa ◽  
2021 ◽  
Vol 529 (1) ◽  
pp. 43-56
Author(s):  
YING GAO ◽  
JUTAMART MONKAI ◽  
ELENI GENTEKAKI ◽  
GUANG-CONG REN ◽  
DHANUSHKA N. WANASINGHE ◽  
...  
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Elongation Factor ◽  
Morphological Characteristics ◽  
Small Subunit ◽  
Morphological Characterization ◽  
Small Subunit Rrna ◽  
Sister Relationship ◽  
Large Subunit Rrna

During a survey of saprobic microfungi in Southwest China, a coelomycetous fungus was found on dead twigs of Jasminum nudiflorum in Kunming, Yunnan Province. Based on a detailed morphological characterization coupled with multi-locus phylogenetic analyses, the fungus was identified as a new species in the genus Dothidea. Phylogenetic analyses using a combined matrix consisting of internal transcribed spacer (ITS), large subunit rRNA (LSU), small subunit rRNA (SSU), beta tubulin (tub2) and translation elongation factor-1 alpha (tef1-α) confirmed its placement in Dothideaceae and revealed a sister relationship to Dothidea eucalypti. The new species is characterized by pycnidial conidiomata, ampulliform or doliiform conidiogenous cells as well as aseptate, subglobose to ovoid, hyaline to pale-brown conidia. Comprehensive descriptions and illustrations are provided. Morphological characteristics of asexual morph taxa in Dothideaceae are also summarized and discussed.

scholarly journals Complete Sequence of the Intronless Mitochondrial Genome of the Saccharomyces cerevisiae Strain CW252

2018 ◽  
Vol 6 (17) ◽  
Author(s):  
Delphine Naquin ◽  
Cristina Panozzo ◽  
Geneviève Dujardin ◽  
Erwin van Dijk ◽  
Yves d’Aubenton-Carafa ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mitochondrial Genome ◽  
Complete Sequence ◽  
Mitochondrial Genomes ◽  
Content Type ◽  
Nuclear Background ◽  
Recombinant Genome ◽  
Mitochondrial Respiratory

ABSTRACT The mitochondrial genomes of Saccharomyces cerevisiae strains contain up to 13 introns. An intronless recombinant genome introduced into the nuclear background of S. cerevisiae strain W303 gave the S. cerevisiae CW252 strain, which is used to model mitochondrial respiratory pathologies. The complete sequence of this mitochondrial genome was obtained using a hybrid assembling methodology.

Ficophagus auriculatae n. sp. (Nematoda: Aphelenchoididae), an associate of the Ficus auriculata-complex in China

Nematology ◽  
2019 ◽  
Vol 21 (5) ◽  
pp. 497-508
Author(s):  
Yongsan Zeng ◽  
Jianfeng Huang ◽  
Dayuan Zhang ◽  
Wensheng Zeng ◽  
Rongrong Shi ◽  
...  
Keyword(s):  
Large Subunit ◽  
Nematode Species ◽  
Botanical Garden ◽  
Small Subunit ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Male Tail ◽  
Small Subunit Rrna Gene ◽  
Tail Tip ◽  
Large Subunit Rrna

Summary A new nematode species was recovered from the syconia of Ficus auriculata-complex, including F. auriculata, F. oligodon and F. hainanensis, from Xishuangbanna Tropical Botanical Garden, China. It is described herein as Ficophagus auriculatae n. sp. and is characterised by possessing the combined characters of a short post-uterine sac, excretory pore located between the metacorpus and the stylet basal knobs, testis multi-reflexed, amoeboid sperm, three pairs of subventral papillae on male tail, rounded male tail tip without mucron, absence of gubernaculum (= apophysis) and sickle-shaped spicules with terminal cucullus. Ficophagus auriculatae n. sp. was differentiated from other sequenced species by the partial small subunit rRNA gene and D2-D3 expansion segments of the large subunit rRNA gene. Phylogenetic analysis with the above-mentioned sequences suggested that F. auriculatae n. sp. has a closer relationship with F. fleckeri in the same highly supported monophyletic clade than with the other sequenced Ficophagus and Schistonchus sensu lato species.

scholarly journals Investigation of the structural basis of the interaction of calpain II with phospholipid and with carbohydrate

1990 ◽  
Vol 265 (2) ◽  
pp. 575-579 ◽  
Author(s):  
C Crawford ◽  
N R Brown ◽  
A C Willis
Keyword(s):  
Large Subunit ◽  
Specific Interaction ◽  
Gel Filtration ◽  
Small Subunit ◽  
Complete Sequence ◽  
Structural Basis ◽  
Proteolytic Degradation ◽  
Amino Acid Sequence Analysis ◽  
Pig Kidney ◽  
Calpain Ii

Two forms of pig kidney calpain II were isolated, both of which appeared to contain an intact 80 kDa large subunit, but which showed specific proteolytic degradation at the N-terminal end of the 30 kDa small subunit. The structure of each of these molecules was investigated by amino acid sequence analysis. The forms corresponded to molecules with small subunits starting at residue 38 (degraded calpain A) and at residue 62 (degraded calpain B) of the complete sequence. These molecules were tested for their ability to interact with phosphatidylinositol and with carbohydrate (agarose gel-filtration media). Calpain and degraded calpain A, but not degraded calpain B, would interact with phosphatidylinositol. Thus the sequence (G)17TAMRILG (residues 38-61) is essential for the interaction. Neither calpain nor the degraded forms of the enzyme showed specific interaction with carbohydrate.

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