scholarly journals Complete mitochondrial genome of Muricea crassa and Muricea purpurea (Anthozoa: Octocorallia) from the eastern tropical Pacific

2016 ◽  
Author(s):  
Angelo Poliseno ◽  
Odalisca Breedy ◽  
Michael Eitel ◽  
Gert Wöerheide ◽  
Hector M. Guzman ◽  
...  
Keyword(s):  
Complete Mitochondrial Genome ◽  
Mitochondrial Protein ◽  
Gc Content ◽  
Tropical Pacific ◽  
Gene Arrangement ◽  
Eastern Tropical Pacific ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Intergenic Regions ◽  
High Level

AbstractWe sequenced the complete mitogenomes of two eastern tropical Pacific gorgonians, Muricea crassa and Muricea purpurea, using NGS technologies. The assembled mitogenomes of M. crassa and M. purpurea were 19,586 bp and 19,358 bp in length, with a GC-content ranging from 36.0% to 36.1%, respectively. The two mitogenomes had the same gene arrangement consisting of 14 protein-coding genes, two rRNAs and one tRNA. Mitogenome identity was 98.5%. The intergenic regions between COB and NAD6 and between NAD5 and NAD4 were polymorphic in length with a high level of nucleotide diversity. Based on a concatenated dataset of 14 mitochondrial protein-coding genes we inferred the phylogeny of 26 octocoral species.

Characterization of the mitochondrial genome of Diphyllobothrium latum (Cestoda: Pseudophyllidea) – implications for the phylogeny of eucestodes

Parasitology ◽  
2006 ◽  
Vol 134 (5) ◽  
pp. 749-759 ◽  
Author(s):  
J.-K. PARK ◽  
K.-H. KIM ◽  
S. KANG ◽  
H. K. JEON ◽  
J.-H. KIM ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Amino Acid Sequences ◽  
Hymenolepis Diminuta ◽  
Rrna Genes ◽  
Gene Arrangement ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Diphyllobothrium Latum

SUMMARYThe complete nucleotide sequence of the mitochondrial genome was determined for the fish tapeworm Diphyllobothrium latum. This genome is 13 608 bp in length and encodes 12 protein-coding genes (but lacks the atp8), 22 transfer RNA (tRNA) and 2 ribosomal RNA (rRNA) genes, corresponding to the gene complement found thus far in other flatworm mitochondrial (mt) DNAs. The gene arrangement of this pseudophyllidean cestode is the same as the 6 cyclophyllidean cestodes characterized to date, with only minor variation in structure among these other genomes; the relative position of trnS2 and trnL1 is switched in Hymenolepis diminuta. Phylogenetic analyses of the concatenated amino acid sequences for 12 protein-coding genes of all complete cestode mtDNAs confirmed taxonomic and previous phylogenetic assessments, with D. latum being a sister taxon to the cyclophyllideans. High nodal support and phylogenetic congruence between different methods suggest that mt genomes may be of utility in resolving ordinal relationships within the cestodes. All species of Diphyllobothrium infect fish-eating vertebrates, and D. latum commonly infects humans through the ingestion of raw, poorly cooked or pickled fish. The complete mitochondrial genome provides a wealth of genetic markers which could be useful for identifying different life-cycle stages and for investigating their population genetics, ecology and epidemiology.

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.

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

2018 ◽  
Vol 4 ◽  
Author(s):  
Helen E. Robertson ◽  
Philipp H. Schiffer ◽  
Maximilian J. Telford
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Protein ◽  
Mitochondrial Genes ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Limited Support ◽  
Cell Layers

Abstract The 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 unique gene order. The data we have analysed 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 of 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.

scholarly journals The complete mitochondrial genome of Pyxicephalus adspersus: high gene rearrangement and phylogenetics of one of the world’s largest frogs

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7532 ◽  
Author(s):  
Yin-Yin Cai ◽  
Shi-Qi Shen ◽  
Li-Xu Lu ◽  
Kenneth B. Storey ◽  
Dan-Na Yu ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Gene Rearrangement ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Protein ◽  
Sub Saharan Africa ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes

The family Pyxicephalidae including two subfamilies (Cacosterninae and Pyxicephalinae) is an ecologically important group of frogs distributed in sub-Saharan Africa. However, its phylogenetic position among the Anura has remained uncertain. The present study determined the complete mitochondrial genome sequence of Pyxicephalus adspersus, the first representative mitochondrial genome from the Pyxicephalinae, and reconstructed the phylogenetic relationships within Ranoidae using 10 mitochondrial protein-coding genes of 59 frog species. The P. adspersus mitochondrial genome showed major gene rearrangement and an exceptionally long length that is not shared with other Ranoidae species. The genome is 24,317 bp in length, and contains 15 protein-coding genes (including extra COX3 and Cyt b genes), four rRNA genes (including extra 12S rRNA and 16S rRNA genes), 29 tRNA genes (including extra tRNALeu (UAG), tRNALeu (UUR), tRNAThr, tRNAPro, tRNAPhe, tRNAVal, tRNAGln genes) and two control regions (CRs). The Dimer-Mitogenome and Tandem duplication and random loss models were used to explain these gene arrangements. Finally, both Bayesian inference and maximum likelihood analyses supported the conclusion that Pyxicephalidae was monophyletic and that Pyxicephalidae was the sister clade of (Petropedetidae + Ptychadenidae).

scholarly journals Assembly and comparative analysis of complete mitochondrial genome sequence of an economic plantSalix suchowensis

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3148 ◽  
Author(s):  
Ning Ye ◽  
Xuelin Wang ◽  
Juan Li ◽  
Changwei Bi ◽  
Yiqing Xu ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Mitochondrial Genome ◽  
Gc Content ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Trna Genes ◽  
Shrub Willow ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Mt Genome

Willow is a widely used dioecious woody plant ofSalicaceaefamily in China. Due to their high biomass yields, willows are promising sources for bioenergy crops. In this study, we assembled the complete mitochondrial (mt) genome sequence ofS. suchowensiswith the length of 644,437 bp using Roche-454 GS FLX Titanium sequencing technologies. Base composition of theS. suchowensismt genome is A (27.43%), T (27.59%), C (22.34%), and G (22.64%), which shows a prevalent GC content with that of other angiosperms. This long circular mt genome encodes 58 unique genes (32 protein-coding genes, 23 tRNA genes and 3 rRNA genes), and 9 of the 32 protein-coding genes contain 17 introns. Through the phylogenetic analysis of 35 species based on 23 protein-coding genes, it is supported thatSalixas a sister toPopulus. With the detailed phylogenetic information and the identification of phylogenetic position, some ribosomal protein genes and succinate dehydrogenase genes are found usually lost during evolution. As a native shrub willow species, this worthwhile research ofS. suchowensismt genome will provide more desirable information for better understanding the genomic breeding and missing pieces of sex determination evolution in the future.

scholarly journals Characterization and comparative analysis among plastome sequences of eight endemic Rubus (Rosaceae) species in Taiwan

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
JiYoung Yang ◽  
Yu-Chung Chiang ◽  
Tsai-Wen Hsu ◽  
Seon-Hee Kim ◽  
Jae-Hong Pak ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Gc Content ◽  
Taxon Sampling ◽  
Phylogenomic Analysis ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Plastome Evolution ◽  
Rosaceae Species ◽  
The Family ◽  
Intergenic Regions

AbstractGenus Rubus represents the second largest genus of the family Rosaceae in Taiwan, with 41 currently recognized species across three subgenera (Chamaebatus, Idaoeobatus, and Malochobatus). Despite previous morphological and cytological studies, little is known regarding the overall phylogenetic relationships among the Rubus species in Taiwan, and their relationships to congeneric species in continental China. We characterized eight complete plastomes of Taiwan endemic Rubus species: subg. Idaeobatus (R. glandulosopunctatus, R. incanus, R. parviaraliifolius, R rubroangustifolius, R. taitoensis, and R. taiwanicolus) and subg. Malachobatus (R. kawakamii and R. laciniastostipulatus) to determine their phylogenetic relationships. The plastomes were highly conserved and the size of the complete plastome sequences ranged from 155,566 to 156,236 bp. The overall GC content ranged from 37.0 to 37.3%. The frequency of codon usage showed similar patterns among species, and 29 of the 73 common protein-coding genes were positively selected. The comparative phylogenomic analysis identified four highly variable intergenic regions (rps16/trnQ, petA/psbJ, rpl32/trnL-UAG, and trnT-UGU/trnL-UAA). Phylogenetic analysis of 31 representative complete plastomes within the family Rosaceae revealed three major lineages within Rubus in Taiwan. However, overall phylogenetic relationships among endemic species require broader taxon sampling to gain new insights into infrageneric relationships and their plastome evolution.

Characterization of the complete mitochondrial genome of a coconut crab, Birgus latro (Linnaeus, 1767) (Decapoda: Anomura: Coenobitidae), from Okinawa, Japan

2020 ◽  
Vol 40 (4) ◽  
pp. 390-400 ◽  
Author(s):  
Werner P Veldsman ◽  
Yaqin Wang ◽  
Jiaojiao Niu ◽  
J Antonio Baeza ◽  
Ka Hou Chu
Keyword(s):  
Indian Ocean ◽  
Mitochondrial Genome ◽  
Control Region ◽  
Complete Mitochondrial Genome ◽  
Gc Content ◽  
Gene Families ◽  
Full Description ◽  
Population Divergence ◽  
Protein Coding ◽  
Protein Coding Genes

Abstract We present a full description and analysis of the complete mitochondrial genome of a Pacific Ocean specimen of the coconut crab Birgus latro (Linnaeus, 1767), the largest extant terrestrial arthropod in the world. Our de novo-assembled mitogenome has a massive 16,161 times organelle read coverage, a length of 16,411 bp, contains 22 tDNAs (20 unique), 13 protein-coding genes, two rDNAs, and a putative control region of length 1,381 bp. The control region contains three microsatellites and two pairs of inverted repeats. Contrary to the mitochondrial sentinel gene concept, two-dimensional nucleotide analysis reveals higher GC-content in cox gene families than in nadh gene families. Moreover, cox gene families are more conserved than nadh gene families among the species of Coenobitidae selected for comparison. Secondary structure prediction of the 22 tDNAs shows major deviations from the cloverleaf pattern, which points to a relatively high rate of mutation in these genes. We also present a repertoire of mitochondrial variation between our male Okinawan coconut crab and an Indian Ocean specimen that consists of one insertion, one deletion, 135 SNPs, three MNPs and nine complex polymorphisms. We provide confirmatory evidence that the superfamily Paguroidea, to which the coconut crab belongs, is polyphyletic, that all the protein-coding genes of B. latro are under purifying selection, and that a Pacific versus Indian Ocean coconut crab population divergence occurred during the Pleistocene.

scholarly journals Complete Mitochondrial Genome Sequence of Bos Frontalis (Gayal) of Bangladesh

2021 ◽  
Author(s):  
Gautam Kumar Deb ◽  
Razia Khatun ◽  
Shakh Mohammed Jahangir Hossain ◽  
Shamsur Rahaman ◽  
Md. Anamul Bahar Bhuiyan ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Related Species ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Gene Arrangement ◽  
Trna Genes ◽  
Closely Related Species ◽  
Protein Coding ◽  
Protein Coding Genes

Abstract Background: Complete mitochondrial genome of Bos frontalis will aid in the investigation of evolutionary links between closely related species. Bos frontalis mitogenome contains 37 genes and a control region. We discover the first complete mitogenome of Bos frontalis found in Bangladesh which was obtained from whole-genome sequencing of Bos frontalis.Results: Bos frontalis mitogenome is 16,347 bp long, with an AT-based nucleotide composition (60.21%). It contains 37 genes, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region (D-loop). This circular genome starts with ND6(negative strand) and ends at ND5(positive strand). Protein coding genes lost 24 bases and tRNA genes gained 27 bases compared to closely related species. Phylogenetic analysis of the mitochondrial genome of 26 closely related species from 8 congeneric species was conducted by the maximum likelihood method with 1000 bootstrap iteration.Conclusion: Our studied Bos frontalis mitochondrial genome has a similar gene arrangement compared with other Bos species. It has almost the same amount of AT and GC content, but notably the ND6 gene lacks AT skew and GC skew than that of the other two comparing species. PCG’s loss in size might be a continuous process of evolution. The mitochondrial genome is regarded as a critical tool for species identification and monitoring populations of conservation concern.

The complete mitochondrial genome of the Dutch elm disease fungus Ophiostoma novo-ulmi subsp. novo-ulmi

2018 ◽  
Vol 64 (5) ◽  
pp. 339-348 ◽  
Author(s):  
Talal George Abboud ◽  
Abdullah Zubaer ◽  
Alvan Wai ◽  
Georg Hausner
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Protein ◽  
Open Reading Frames ◽  
Dutch Elm Disease ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Statistical Support ◽  
Size Variability ◽  
Reading Frames

Ophiostoma novo-ulmi, a member of the Ophiostomatales (Ascomycota), is the causal agent of the current Dutch elm disease pandemic in Europe and North America. The complete mitochondrial genome (mtDNA) of Ophiostoma novo-ulmi subsp. novo-ulmi, the European component of O. novo-ulmi, has been sequenced and annotated. Gene order (synteny) among the currently available members of the Ophiostomatales was examined and appears to be conserved, and mtDNA size variability among the Ophiostomatales is due in part to the presence of introns and their encoded open reading frames. Phylogenetic analysis of concatenated mitochondrial protein-coding genes yielded phylogenetic estimates for various members of the Ophiostomatales, with strong statistical support showing that mtDNA analysis may provide valuable insights into the evolution of the Ophiostomatales.

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