Comparative Analysis of the Complete Mitochondrion of Chlorophytum Comosum with 9 Other Species

Abstract Chlorophytum comosum belongs to genus Chlorophytum of family Asparagaceae that has more than 215 species. it is among 120 plant species assayed for phytoremediation of pollutants from indoor air. It has the ability to remove formaldehyde, nitrogen dioxide, carbon oxide, ozone, benzene, toluene, cigarette smoke and ammonia. It also is an important Chinese tradition medicine material. Aim to get more information about its mitochondrial genome, we sequenced the complete mitochondrial genome of C. comosum. The length of mitochondrial genome was 950316 bp with 36 protein coding genes, 5 rRNAs and 21 tRNAs. Although it has the biggest mitochondrial genome, the total PCGs content were the second least. C. comosum had the most repeats sequence and it may effect the size of mitochondrial genome, but base the result we found that the quantity of repeats sequence could not have the positive correlation with the mitochondrial size. Compared with other 9 species , we found in the mitochondrial genome of C. comosum, there were at least one PCGs suffered from the positive selection after divergence. Finally, the result of phylogenetic showed that C. comosum did not have colesd relationship with other species.

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

Journal of Helminthology ◽

10.1017/s0022149x18000871 ◽

2018 ◽

Vol 94 ◽

Cited By ~ 3

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.

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Phylogenetic relationships and taxonomic position of genus Hyperacrius (Rodentia: Arvicolinae) from Kashmir based on evidences from analysis of mitochondrial genome and study of skull morphology

PeerJ ◽

10.7717/peerj.10364 ◽

2020 ◽

Vol 8 ◽

pp. e10364

Author(s):

Natalia I. Abramson ◽

Fedor N. Golenishchev ◽

Semen Yu. Bodrov ◽

Olga V. Bondareva ◽

Evgeny A. Genelt-Yanovskiy ◽

...

Keyword(s):

Mitochondrial Genome ◽

De Novo ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Morphological Characters ◽

Molecular Data ◽

Phylogenetic Position ◽

Skull Morphology ◽

Protein Coding ◽

Protein Coding Genes

In this article, we present the nearly complete mitochondrial genome of the Subalpine Kashmir vole Hyperacrius fertilis (Arvicolinae, Cricetidae, Rodentia), assembled using data from Illumina next-generation sequencing (NGS) of the DNA from a century-old museum specimen. De novo assembly consisted of 16,341 bp and included all mitogenome protein-coding genes as well as 12S and 16S RNAs, tRNAs and D-loop. Using the alignment of protein-coding genes of 14 previously published Arvicolini tribe mitogenomes, seven Clethrionomyini mitogenomes, and also Ondatra and Dicrostonyx outgroups, we conducted phylogenetic reconstructions based on a dataset of 13 protein-coding genes (PCGs) under maximum likelihood and Bayesian inference. Phylogenetic analyses robustly supported the phylogenetic position of this species within the tribe Arvicolini. Among the Arvicolini, Hyperacrius represents one of the early-diverged lineages. This result of phylogenetic analysis altered the conventional view on phylogenetic relatedness between Hyperacrius and Alticola and prompted the revision of morphological characters underlying the former assumption. Morphological analysis performed here confirmed molecular data and provided additional evidence for taxonomic replacement of the genus Hyperacrius from the tribe Clethrionomyini to the tribe Arvicolini.

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The complete mitochondrial genome of a cold seep gastropod Phymorhynchus buccinoides (Neogastropoda: Conoidea: Raphitomidae)

PLoS ONE ◽

10.1371/journal.pone.0242541 ◽

2020 ◽

Vol 15 (11) ◽

pp. e0242541

Author(s):

Lvpei Du ◽

Shanya Cai ◽

Jun Liu ◽

Ruoyu Liu ◽

Haibin Zhang

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Cold Seep ◽

Start Codon ◽

Rrna Genes ◽

Trna Genes ◽

Protein Coding ◽

Future Studies ◽

Protein Coding Genes ◽

High Support

Phymorhynchus is a genus of deep-sea snails that are most distributed in hydrothermal vent or cold seep environments. In this study, we presented the complete mitochondrial genome of P. buccinoides, a cold seep snail from the South China Sea. It is the first mitochondrial genome of a cold seep member of the superfamily Conoidea. The mitochondrial genome is 15,764 bp in length, and contains 13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes. These genes are encoded on the positive strand, except for 8 tRNA genes that are encoded on the negative strand. The start codon ATG and 3 types of stop codons, TAA, TAG and the truncated termination codon T, are used in the 13 PCGs. All 13 PCGs in the 26 species of Conoidea share the same gene order, while several tRNA genes have been translocated. Phylogenetic analysis revealed that P. buccinoides clustered with Typhlosyrinx sp., Eubela sp., and Phymorhynchus sp., forming the Raphitomidae clade, with high support values. Positive selection analysis showed that a residue located in atp6 (18 S) was identified as the positively selected site with high posterior probabilities, suggesting potential adaption to the cold seep environment. Overall, our data will provide a useful resource on the evolutionary adaptation of cold seep snails for future studies.

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

Scientific Reports ◽

10.1038/s41598-021-82561-1 ◽

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.

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

Parasitology ◽

10.1017/s003118200600206x ◽

2006 ◽

Vol 134 (5) ◽

pp. 749-759 ◽

Cited By ~ 19

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.

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

10.1101/282285 ◽

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.

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Characterization of the mitochondrial genome of Analcellicampa xanthosoma gen. et sp. nov. (Hymenoptera: Tenthredinidae)

PeerJ ◽

10.7717/peerj.6866 ◽

2019 ◽

Vol 7 ◽

pp. e6866 ◽

Cited By ~ 3

Author(s):

Gengyun Niu ◽

Yaoyao Zhang ◽

Zhenyi Li ◽

Meicai Wei

Keyword(s):

Mitochondrial Genome ◽

New Genus ◽

Complete Mitochondrial Genome ◽

Sister Group ◽

Mitochondrial Genomes ◽

Protein Coding ◽

Protein Coding Genes ◽

A New Species ◽

High Support

A new genus with a new species of the tribe Hoplocampini of Hoplocampinae was described from China: Analcellicampa xanthosoma Wei & Niu, gen. et sp. nov. Hoplocampa danfengensis G. Xiao 1994 was designated as the type species of the new genus. The characters of Analcellicampa danfengensis (G. Xiao) comb. nov. were briefly discussed. A key to the tribes and known genera of Hoplocampinae was provided. The nearly complete mitochondrial genome of A. xanthosoma was characterized as having a length of 15,512 bp and containing 37 genes (22 tRNAs, 13 protein-coding genes (PCGs), and 2 rRNAs). The gene order of this new specimen was the same as that in the inferred insect ancestral mitochondrial genome. All PCGs were initiated by ATN codons and ended with TAA or T stop codons. All tRNAs had a typical cloverleaf secondary structure, except for trnS1. Remarkably, the helices H991 of rrnS and H47 of rrnL were redundant, while helix H563 of rrnL was highly conserved. A phylogeny based on previously reported symphytan mitochondrial genomes showed that A. xanthosoma is a sister group to Monocellicampa pruni, with high support values. We suggest that A. xanthosoma and M. pruni belong to the tribe Hoplocampini of Hoplocampinae.

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Mitochondrial genome of the critically endangered Baer’s Pochard, Aythya baeri, and its phylogenetic relationship with other Anatidae species

Scientific Reports ◽

10.1038/s41598-021-03868-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Dawei Liu ◽

Yongwu Zhou ◽

Yiling Fei ◽

Chunping Xie ◽

Senlin Hou

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

The Other ◽

Rrna Genes ◽

Trna Genes ◽

Protein Coding ◽

Protein Coding Genes ◽

Recent Estimate ◽

Maximum Likelihood Methods ◽

Taxonomic Studies

AbstractHistorically, the diving duck, Baer’s Pochard (Aythya baeri) was widely distributed in East and South Asia, but according to a recent estimate, its global population is now less than 1000 individuals. To date, the mitochondrial genome of A. baeri has not been deposited and is not available in GenBank. Therefore, we aimed to sequence the complete mitochondrial genome of this species. The genome was 16,623 bp in length, double stranded, circular in shape, and contained 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one non-coding control region. Many structural and compositional similarities were discovered between A. baeri and the other three Aythya mitochondrial genomes. Among 13 protein-coding genes of the four Aythya species, the fastest-evolving gene was ATP8 while the slowest-evolving gene was COII. Furthermore, the phylogenetic tree of Anatidae based on Bayesian inference and maximum likelihood methods showed that the relationships among 15 genera of the Anatidae family were as follows: Dendrocygna was an early diverging lineage that was fairly distant from the other ingroup taxa; Cygnus, Branta, and Anser were clustered into one branch that corresponded to the Anserinae subfamily; and Aythya, Asarcornis, Netta, Anas, Mareca, Mergus, Lophodytes, Bucephala, Tadorna, Cairina, and Aix were clustered into another branch that corresponded to the Anatinae subfamily. Our target species and three other Aythya species formed a monophyletic group. These results provide new mitogenomic information to support further phylogenetic and taxonomic studies and genetic conservation of Anatidae species.

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Characterization and comparative analysis of the complete mitochondrial genome of Azygia hwangtsiyui Tsin, 1933 (Digenea), the first for a member of the family Azygiidae

ZooKeys ◽

10.3897/zookeys.945.49681 ◽

2020 ◽

Vol 945 ◽

pp. 1-16

Author(s):

Yuan-An Wu ◽

Jin-Wei Gao ◽

Xiao-Fei Cheng ◽

Min Xie ◽

Xi-Ping Yuan ◽

...

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Nucleotide Composition ◽

Amino Acid Sequences ◽

Phylogenetic Study ◽

Protein Coding ◽

Protein Coding Genes ◽

The Family ◽

Close Relationship ◽

Rna Genes

Azygia hwangtsiyui (Trematoda, Azygiidae), a neglected parasite of predatory fishes, is little-known in terms of its molecular epidemiology, population ecology and phylogenetic study. In the present study, the complete mitochondrial genome of A. hwangtsiyui was sequenced and characterized: it is a 13,973 bp circular DNA molecule and encodes 36 genes (12 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes) as well as two non-coding regions. The A+T content of the A. hwangtsiyui mitogenome is 59.6% and displays a remarkable bias in nucleotide composition with a negative AT skew (–0.437) and a positive GC skew (0.408). Phylogenetic analysis based on concatenated amino acid sequences of twelve protein-coding genes reveals that A. hwangtsiyui is placed in a separate clade, suggesting that it has no close relationship with any other trematode family. This is the first characterization of the A. hwangtsiyui mitogenome, and the first reported mitogenome of the family Azygiidae. These novel datasets of the A. hwangtsiyui mt genome represent a meaningful resource for the development of mitochondrial markers for the identification, diagnostics, taxonomy, homology and phylogenetic relationships of trematodes.

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The complete mitochondrial genome of stag beetle Lucanus cervus (Coleoptera: Lucanidae) and phylogenetic analysis

PeerJ ◽

10.7717/peerj.8274 ◽

2019 ◽

Vol 7 ◽

pp. e8274 ◽

Cited By ~ 4

Author(s):

Dan Chen ◽

Jing Liu ◽

Luca Bartolozzi ◽

Xia Wan

Keyword(s):

Mitochondrial Genome ◽

Bayesian Methods ◽

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Illumina Platform ◽

Protein Coding ◽

Protein Coding Genes ◽

Rna Genes ◽

Generation Sequencing

Background The stag beetle Lucanus cervus (Coleoptera: Lucanidae) is widely distributed in Europe. Habitat loss and fragmentation has led to significant reductions in numbers of this species. In this study, we sequenced the complete mitochondrial genome of L. cervus and reconstructed phylogenetic relationships among Lucanidae using complete mitochondrial genome sequences. Methods Raw data sequences were generated by the next generation sequencing using Illumina platform from genomic DNA of L. cervus. The mitochondrial genome was assembled by IDBA and annotated by MITOS. The aligned sequences of mitochondrial genes were partitioned using PartitionFinder 2. Phylogenetic relationships among 19 stag beetle species were constructed using Maximum Likelihood (ML) method implemented in IQ-TREE web server and Bayesian method implemented in PhyloBayes MPI 1.5a. Three scarab beetles were used as outgroups. Results The complete mitochondrial genome of L. cervus is 20,109 bp in length, comprising 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNAs and a control region. The A + T content is 69.93% for the majority strand. All protein-coding genes start with the typical ATN initiation codons except for cox1, which uses AAT. Phylogenetic analyses based on ML and Bayesian methods shown consistent topologies among Lucanidae.

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