scholarly journals Complete Mitochondrial Genome of Phoneutria Boliviensis (Araneae, Ctenidae): New Insights Into the Phylogeny and Evolution of Spider

2021 ◽  
Author(s):  
Carlos Fernando Prada ◽  
Lida Marcela Franco ◽  
Felipe Cabarcas
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
High Rate ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Order Analysis ◽  
Phylogeny And Evolution ◽  
The Relationship

Abstract Spiders are the most abundant land predators and megadiverse on earth. In recent years, the mitochondrial genome has been sequenced, mainly for ecological and commercial purposes, reporting some level of rearrangements in this genome. However, there is poor genetic information in several taxonomic families of spiders. The aim of this study was to obtain the sequence of the complete genome of Phoneutria boliviensis and, based on this, extract the mitogenomes of other species of the family Ctenidae from published transcriptomes to perform a comparative study among spider species to determine the relationship between the level of mitochondrial rearrangement and its possible relationship with molecular variability in spiders. Complete mitochondrial genomes of eighteen spiders (including nine Ctenidae species) were obtained by two different methodologies (sequencing and transcriptome extraction). Fifty-eight spider mitochondrial genomes were downloaded from the NCBI database for gene order analysis. After verifying the annotation of each mitochondrial gene, a phylogeny and gene order, analysis from 76 spider mitochondrial genomes was obtained. Our results show a high rate of annotation error in the mitochondrial genomes of spiders published in databases, which could lead to false phylogenetic relationships. Moreover, to provide new mitochondrial genomes in spiders by two different methodologies to obtain them, our analysis identifies six different mitochondrial architectures among all spiders. Translocation or tandem duplication random loss (TDRL) events in tRNA genes were identified to explain the evolution of the spider mitochondrial genome. In addition, our findings provide new insights into spider mitochondrial evolution.

scholarly journals Comprehensive Analyses of the Complete Mitochondrial Genome of Figulus binodulus (Coleoptera: Lucanidae)

2020 ◽  
Vol 20 (5) ◽  
Author(s):  
Jungmo Lee ◽  
Jonghyun Park ◽  
Hong Xi ◽  
Jongsun Park
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Transfer Rnas ◽  
Mitochondrial Gene Order ◽  
Rna Genes ◽  
Simple Sequence

Abstract Figulus binodulus Waterhouse is a small stag beetle distributed in East Asia. We determined the first mitochondrial genome of F. binodulus of which is 16,261-bp long including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single large noncoding region of 1,717 bp. Gene order of F. binodulus is identical to the ancestral insect mitochondrial gene order as in most other stag beetle species. All of 22 tRNAs could be shaped into typical clover-leaf structure except trnSer1. Comparative analyses of 21 Lucanidae mitochondrial genomes was conducted in aspect of their length and AT-GC ratio. Nucleotide diversities analyses provide that cox1 and cox2 in Lucanidae are less diverse than those of Scarabaeoidea. Fifty simple sequence repeats (SSRs) were identified on F. binodulus mitochondrial genome. Comparative analysis of SSRs among five mitochondrial genomes displayed similar trend along with SSR types. Figulus binodulus was sister to all other available family Lucanidae species in the phylogenetic tree.

scholarly journals The first mitochondrial genome of the genus Exhippolysmata (Decapoda: Caridea: Lysmatidae), with gene rearrangements and phylogenetic associations in Caridea

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ying-ying Ye ◽  
Jing Miao ◽  
Ya-hong Guo ◽  
Li Gong ◽  
Li-hua Jiang ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Bootstrap Support ◽  
Trna Genes ◽  
Gene Rearrangements ◽  
Phylogenetic Studies ◽  
Gc Skew ◽  
Strong Bootstrap Support

AbstractThe complete mitochondrial genome (mitogenome) of animals can provide useful information for evolutionary and phylogenetic analyses. The mitogenome of the genus Exhippolysmata (i.e., Exhippolysmata ensirostris) was sequenced and annotated for the first time, its phylogenetic relationship with selected members from the infraorder Caridea was investigated. The 16,350 bp mitogenome contains the entire set of 37 common genes. The mitogenome composition was highly A + T biased at 64.43% with positive AT skew (0.009) and negative GC skew (− 0.199). All tRNA genes in the E. ensirostris mitogenome had a typical cloverleaf secondary structure, except for trnS1 (AGN), which appeared to lack the dihydrouridine arm. The gene order in the E. ensirostris mitogenome was rearranged compared with those of ancestral decapod taxa, the gene order of trnL2-cox2 changed to cox2-trnL2. The tandem duplication-random loss model is the most likely mechanism for the observed gene rearrangement of E. ensirostris. The ML and BI phylogenetic analyses place all Caridea species into one group with strong bootstrap support. The family Lysmatidae is most closely related to Alpheidae and Palaemonidae. These results will help to better understand the gene rearrangements and evolutionary position of E. ensirostris and lay a foundation for further phylogenetic studies of Caridea.

scholarly journals The mitochondrial genome of Dipetalonema gracile from a squirrel monkey in China

2018 ◽  
Vol 94 ◽  
Author(s):  
P. Zhang ◽  
R.K. Ran ◽  
A.Y. Abdullahi ◽  
X.L. Shi ◽  
Y. Huang ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Squirrel Monkey ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Rrna Genes ◽  
Saimiri Sciureus ◽  
Trna Genes ◽  
Loop Structure ◽  
Protein Coding ◽  
Protein Coding Genes

AbstractDipetalonema gracile is a common parasite in squirrel monkeys (Saimiri sciureus), which can cause malnutrition and progressive wasting of the host, and lead to death in the case of massive infection. This study aimed to identify a suspected D. gracile worm from a dead squirrel monkey by means of molecular biology, and to amplify its complete mitochondrial genome by polymerase chain reaction (PCR) and sequence analysis. The results identified the worm as D. gracile, and the full length of its complete mitochondrial genome was 13,584 bp, which contained 22 tRNA genes, 12 protein-coding genes, two rRNA genes, one AT-rich region and one small non-coding region. The nucleotide composition included A (16.89%), G (20.19%), T (56.22%) and C (6.70%), among which A + T = 73.11%. The 12 protein-coding genes used TTG and ATT as start codons, and TAG and TAA as stop codons. Among the 22 tRNA genes, only trnS1AGN and trnS2UCN exhibited the TΨC-loop structure, while the other 20 tRNAs showed the TV-loop structure. The rrnL (986 bp) and rrnS (685 bp) genes were single-stranded and conserved in secondary structure. This study has enriched the mitochondrial gene database of Dipetalonema and laid a scientific basis for further study on classification, and genetic and evolutionary relationships of Dipetalonema nematodes.

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 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.

The first complete mitochondrial genome of Pygopodidae (Aprasia parapulchella Kluge)

2015 ◽  
Vol 63 (2) ◽  
pp. 111 ◽  
Author(s):  
Anna J. MacDonald ◽  
Theresa Knopp ◽  
Mitzy Pepper ◽  
J. Scott Keogh ◽  
Stephen D. Sarre
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Rrna Genes ◽  
Trna Genes ◽  
Base Pairs ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Typical Vertebrate

The Pygopodidae comprise an enigmatic group of legless lizards endemic to the Australo-Papuan region. Here we present the first complete mitochondrial genome for a member of this family, Aprasia parapulchella, from Australia. The mitochondrial genome of A. parapulchella is 16 528 base pairs long and contains 13 protein-coding genes, 22 tRNA genes, two rRNA genes and the control region, conforming to the typical vertebrate gene order. The overall mitochondrial nucleotide composition is 31.7% A, 24.5% T, 30.5% C and 13.2% G. This corresponds to a total A+T content of 56.3%, which is similar to that of other squamate lizard genomes.

scholarly journals Genome Characterization, Comparison and Phylogenetic Analysis of Complete Mitochondrial Genome of Evolvulus alsinoides Reveals Highly Rearranged Gene Order in Solanales

Life ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 769
Author(s):  
Pattayampadam Ramakrishnan Shidhi ◽  
Vadakkemukadiyil Chellappan Biju ◽  
Sasi Anu ◽  
Chandrasekharan Laila Vipin ◽  
Kumar Raveendran Deelip ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Complete Mitochondrial Genome ◽  
Genome Structure ◽  
Rrna Genes ◽  
Formation Mechanisms ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Evolvulus Alsinoides

Mitogenome sequencing provides an understanding of the evolutionary mechanism of mitogenome formation, mechanisms driving plant gene order, genome structure, and migration sequences. Data on the mitochondrial genome for family Convolvulaceae members is lacking. E. alsinoides, also known as shankhpushpi, is an important medicinal plant under the family Convolvulaceae, widely used in the Ayurvedic system of medicine. We identified the mitogenome of E. alsinoides using the Illumina mate-pair sequencing platform, and annotated using bioinformatics approaches in the present study. The mitogenome of E. alsinoides was 344184 bp in length and comprised 46 unique coding genes, including 31 protein-coding genes (PCGs), 12 tRNA genes, and 3 rRNA genes. The secondary structure of tRNAs shows that all the tRNAs can be folded into canonical clover-leaf secondary structures, except three trnW, trnG, and trnC. Measurement of the skewness of the nucleotide composition showed that the AT and GC skew is positive, indicating higher A’s and G’s in the mitogenome of E. alsinoides. The Ka/Ks ratios of 11 protein-coding genes (atp1, ccmC, cob, cox1, rps19, rps12, nad3, nad9, atp9, rpl5, nad4L) were <1, indicating that these genes were under purifying selection. Synteny and gene order analysis were performed to identify homologous genes among the related species. Synteny blocks representing nine genes (nad9, nad2, ccmFc, nad1, nad4, nad5, matR, cox1, nad7) were observed in all the species of Solanales. Gene order comparison showed that a high level of gene rearrangement has occurred among all the species of Solanales. The mitogenome data obtained in the present study could be used as the Convolvulaceae family representative for future studies, as there is no complex taxonomic history associated with this plant.

scholarly journals Linear Mitochondrial genome in Anthozoa (Cnidaria): A case study in Ceriantharia

2018 ◽  
Author(s):  
Sergio N Stampar ◽  
Michael B Broe ◽  
Jason Macrander ◽  
Adam M Reitzel ◽  
Marymegan Daly
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Mitochondrial Gene ◽  
Phylogenetic Position ◽  
Mitochondrial Genomes ◽  
Gene Sequences ◽  
Phylogenetic Placement ◽  
Organellar Genome ◽  
Linear Mitochondrial Genome

Sequences and structural attributes of mitochondrial genomes have played a key role in the clarification of relationships among Cnidaria, a key phylum of early-diverging animals. Among the major lineages of Cnidaria, Ceriantharia ("tube anemones") remains one of the most enigmatic groups in terms of its phylogenetic position. We sequenced the mitochondrial genomes of two ceriantharians to see whether the complete organellar genome would provide more support for the phylogenetic placement of Ceriantharia. For both ceriantharian species studied, the mitochondrial gene sequences could not be assembled into a circular genome. Instead, our analyses suggest both species have fragmented mitochondrial genomes consisting of multiple linear fragments. Linear mitogenomes are characteristic of members of Medusozoa, one of the major lineages of Cnidaria, but are unreported for Anthozoa, which includes the Ceriantharia. The number of fragments and the variation in gene order between species is much greater in Ceriantharia than among Medusozoa. The novelty of the mitogenomic structure in Ceriantharia highlights the distinctiveness of this lineage but, because it appears to be both unique to and diverse within Ceriantharia, it is uninformative about the phylogenetic position of Ceriantharia relative to other anthozoan groups.

scholarly journals Mitochondrial Genome Sequence of Phytophthora sansomeana and Comparative Analysis of Phytophthora Mitochondrial Genomes

2020 ◽  
Author(s):  
Guohong Cai ◽  
Steven R. Scofield
Keyword(s):  
Mitochondrial Genome ◽  
Ribosomal Proteins ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Mitochondrial Genomes ◽  
Phylogenomic Analysis ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Circular Molecule

ABSTRACTPhytophthora sansomeana infects soybean and causes root rot. It was recently separated from the species complex P. megasperma sensu lato. In this study, we sequenced and annotated its complete mitochondrial genome and compared it to that of nine other Phytophthora species. The genome was assembled into a circular molecule of 39,618 bp with a 22.03% G+C content. Forty-two protein coding genes, 25 tRNA genes and two rRNA genes were annotated in this genome. The protein coding genes include 14 genes in the respiratory complexes, four ATP synthetase genes, 16 ribosomal proteins genes, a tatC translocase gene, six conserved ORFs and a unique orf402. The tRNA genes encode tRNAs for 19 amino acids. Comparison among mitochondrial genomes of 10 Phytophthora species revealed three inversions, each covering multiple genes. These genomes were conserved in gene content with few exceptions. A 3’ truncated atp9 gene was found in P. nicotianae. All 10 Phytophthora species, as well as other oomycetes and stramenopiles, lacked tRNA genes for threonine in their mitochondria. Phylogenomic analysis using the mitochondrial genomes supported or enhanced previous findings of the phylogeny of Phytophthora spp.

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