scholarly journals The Insights into Mitochondrial Genomes of Sunflowers

Plants ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1774
Author(s):  
Maksim S. Makarenko ◽  
Denis O. Omelchenko ◽  
Alexander V. Usatov ◽  
Vera A. Gavrilova
Keyword(s):  
Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Nuclear Genome ◽  
Jerusalem Artichoke ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Genetic Studies ◽  
Protein Coding ◽  
Significant Difference ◽  
Complete Mitochondrial Genomes

The significant difference in the mtDNA size and structure with simultaneous slow evolving genes makes the mitochondrial genome paradoxical among all three DNA carriers in the plant cell. Such features make mitochondrial genome investigations of particular interest. The genus Helianthus is a diverse taxonomic group, including at least two economically valuable species—common sunflower (H. annuus) and Jerusalem artichoke (H. tuberosus). The successful investigation of the sunflower nuclear genome provided insights into some genomics aspects and significantly intensified sunflower genetic studies. However, the investigations of organelles’ genetic information in Helianthus, especially devoted to mitochondrial genomics, are presented by limited studies. Using NGS sequencing, we assembled the complete mitochondrial genomes for H. occidentalis (281,175 bp) and H. tuberosus (281,287 bp) in the current investigation. Besides the master circle chromosome, in the case of H. tuberosus, the 1361 bp circular plasmid was identified. The mitochondrial gene content was found to be identical for both sunflower species, counting 32 protein-coding genes, 3 rRNA, 23 tRNA genes, and 18 ORFs. The comparative analysis between perennial sunflowers revealed common and polymorphic SSR and SNPs. Comparison of perennial sunflowers with H. annuus allowed us to establish similar rearrangements in mitogenomes, which have possibly been inherited from a common ancestor after the divergence of annual and perennial sunflower species. It is notable that H. occidentalis and H. tuberosus mitogenomes are much more similar to H. strumosus than H. grosseserratus.

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 Genomes of Three Mangifera Species, Their Genomic Structure And Gene Transfer From Chloroplast Genomes

2021 ◽  
Author(s):  
Yingfeng Niu ◽  
Chengwen Gao ◽  
Jin Liu
Keyword(s):  
Mitochondrial Genome ◽  
Genomic Structure ◽  
Mangifera Indica ◽  
Gene Content ◽  
Rrna Genes ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Chloroplast Genomes

Abstract BackgroundAmong the Mangifera species, mango (Mangifera indica) is an important commercial fruit crop. However, very few studies have been conducted on the Mangifera mitochondrial genome. This study reports and compares the newly sequenced mitochondrial genomes of three Mangifera species. Results Mangifera mitochondrial genomes showed partial similarities in the overall size, genomic structure, and gene content. Specifically, the genomes are circular and contain about 63-69 predicted functional genes, including five ribosomal RNA (rRNA) genes and 24-27 transfer RNA (tRNA) genes. The GC contents of the Mangifera mitochondrial genomes are similar, ranging from 44.42–44.66%. Leucine (Leu) and serine (Ser) are the most frequently used, while tryptophan (Trp) and cysteine (Cys) are the least used amino acids among the protein-coding genes in Mangifera mitochondrial genomes. We also identified 7-10 large chloroplast genomic fragments in the mitochondrial genome, ranging from 1407-6142 bp. Additionally, four intact mitochondrial tRNAs genes (tRNA-Cys, tRNA-Trp, tRNA-Pro, and tRNA-Met) and intergenic spacer regions were identified. Phylogenetic analysis based on the common protein-coding genes of most branches provided a high support value. ConclusionsWe sequenced and compared the mitochondrial genomes of three Mangifera species. The results showed that the gene content of Mangifera mitochondrial genomes is similar across various species. Gene transferred from the chloroplast genome to the mitochondrial genome were identified. This study provides valuable information for evolutionary and molecular studies of Mangifera and a basis for further studies on genomic breeding of mango.

The Complete Mitochondrial Genomes of two Flying Fishes, Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii

2020 ◽  
Author(s):  
Liyan Qu ◽  
Heng Zhang ◽  
Fengying Zhang ◽  
Wei Wang ◽  
Fenghua Tang ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Flying Fishes ◽  
Complete Mitochondrial Genomes

Background: Genome-scale approaches have played a significant role in the analysis of evolutionary relationships. Because of rich polymorphisms, high evolutionary rate and rare recombination, mitochondrial DNA sequences are commonly considered as effective markers for estimating population genetics, evolutionary and phylogenetic relationships. Flying fishes are important components of epipelagic ecosystems. Up to now, only few complete mitochondrial genomes of flying fishes have been reported. In the present study, the complete mitochondrial DNA sequences of the Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii had been determined. Methods: Based on the published mitogenome of Cheilopogon atrisignis (GenBank: KU360729), fifteen pairs of primers were designed by the software Primer Premier 5.0 to get the complete mitochondrial genomes of two flying fishes. According to the reported data, the phylogenetic position of two flying fishes were detected using the conserved 12 protein-coding genes. Result: The complete mitochondrial genomes of Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii are determined. They are 16532bp and 16525bp in length, respectively. And they both consists of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a control region. The OL regions are conserved in these two flying fishes and might have no function. From the tree topologies, we found C.p. japonicus and H. rondeletii clustered in a group. The findings of the study would contribute to the phylogenetic classification and the genetic conservation management of C.p. japonicus and H. rondeletii.

scholarly journals Ten complete mitochondrial genomes of Gymnocharacini (Stethaprioninae, Characiformes): evolutionary relationships and a repetitive element in the Control Region (D-loop)

2020 ◽  
Author(s):  
Rubens Pasa ◽  
Fabiano Bezerra Menegídio ◽  
Igor Henrique Rodrigues-Oliveira ◽  
Iuri Batista da Silva ◽  
Matheus Lewi Cruz Bonaccorsi de Campos ◽  
...  
Keyword(s):  
Neotropical Region ◽  
Rrna Genes ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Raw Data ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Species Complexes ◽  
D Loop ◽  
Complete Mitochondrial Genomes

AbstractWe are presenting the complete mitogenomes of eight fish species/cytotypes from Neotropical region belonging to the Astyanax and Psalidodon genus: A. aeneus, A. altiparanae, P. fasciatus (from two locations - Upper Paraná and São Francisco river basins), A. lacustris, P. rivularis (two cytotypes) and P. rioparanaibano. We perform the whole-genome sequencing for six of these species in a Novaseq 6000 - by Illumina, meanwhile two genomes were assembled from raw data available in databases. Plus, we reassembled and annotated the mitochondrial genomes for A. mexicanus and P. paranae, both already described and with raw data available online. All the genomes presented the same organization, with 13 protein-coding genes, 22 tRNA genes and two rRNA genes. Aiming to contribute to the understanding of the several cryptic species complexes and phylogeny of the genus, we perform Bayesian analysis using the 13 protein-coding genes from these species, plus Deuterodon giton and using a Brycon species as outgroup.

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.

Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genomes of Two Tiny Necrophagous Phorid Flies, Metopina sagittata and Puliciphora borinquenensis (Diptera: Phoridae)

2021 ◽  
Author(s):  
Shu-Tong Dai ◽  
Dian-Xing Feng ◽  
Da-Peng Sun
Keyword(s):  
Mitochondrial Genome ◽  
Species Identification ◽  
Stop Codon ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Genomes ◽  
Base Pairs ◽  
Protein Coding ◽  
Phylogenetic Studies ◽  
Rna Genes ◽  
Complete Mitochondrial Genomes

Abstract The mitochondrial genome is frequently used for species identification and phylogenetic studies. In this study, we first sequenced and annotated the complete mitochondrial genomes of two phorid species that are forensically important in buried or enclosed environments: Metopina sagittata (Liu) and Puliciphora borinquenensis (Wheeler). The complete mitochondrial genome sequences of M. sagittata and P. borinquenensis were 15,640 bp with an A+T content of 75.97% and 15,429 bp with an A+T content of 75.38%, respectively. Their circular genomes both contained 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region located between rrnS and trnI which was 808 bp for M. sagittata and 746 bp for P. borinquenensis. All the PCGs of both species started with ATN codons except for cox1 which used TTG codon. In addition to the common stop codon TAA and TAG, the incomplete stop codon T was used in two PCGs (cox1 and nad4) of M. sagittata and five PCGs (cox1, cox2, cox3, nad5, and nad4) of P. borinquenensis. There were 3 and 10 mismatched base pairs in the tRNA secondary structures from M. sagittata and P. borinquenensis, respectively. Both maximum likelihood and Bayesian inference analyses indicated that Platypezidae and Phoridae are sister taxa. M. sagittata is closely related to P. borinquenensis within the subfamily Metopininae. This work enhances the databases of Phoridae genomes and contributes to the further study of species identification and phylogenetics of this family.

The mitochondrial genomes of Panorpidae: sequence, structure and phylogenetic analysis

2020 ◽  
Author(s):  
Yuan Hua ◽  
Ning Li ◽  
Jie Chen ◽  
Bao-Zhen Hua ◽  
Shi-Heng Tao
Keyword(s):  
Nucleotide Diversity ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Sequence Structure ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Gc Skew ◽  
Paraphyletic Group ◽  
Complete Mitogenome ◽  
Complete Mitochondrial Genomes

Abstract Background: Mitochondrial genomes play a significant role in reconstructing phylogenetic relationships and revealing molecular evolution in insects. However, only two species of Panorpidae have been documented for mitochondrial genomes in Mecoptera to date.Results: We obtained complete mitochondrial genomes of 17 species of Panorpidae. The results show that the complete mitogenome sequences of Panorpidae all contain 37 genes (13 protein-coding genes (PCGs), two rRNAs, 22 tRNAs) and one control region. The mitogenomes exhibit a strong AT bias. The AT-skew can either be slightly positive or slightly negative, while the GC-skew is usually negative. The 22 tRNA genes can fold into a common cloverleaf secondary structure except trnS1. The sliding window and genetic distance analyses demonstrate highly variable nucleotide diversity among the 13 protein-coding genes, with comparatively low evolutionary rate of cox1, cox2 and nad1, and high variability of nad2 and nad6. The phylogeny of Panorpidae can be presented as (Neopanorpa + Furcatopanorpa) + (Dicerapanorpa + (Panorpa debilis + (Sinopanorpa + (Cerapanorpa + Panorpa)))).Conclusions: Our analyses indicate that the genes nad2 and nad6 can be regarded as potential markers for population genetics and species delimitation in Panorpidae. Panorpa is reconfirmed a paraphyletic group.

Two complete mitochondrial genomes of Crocodylus and implications for crocodilians phylogeny

2010 ◽  
Vol 31 (3) ◽  
pp. 299-309 ◽  
Author(s):  
Peng Yan ◽  
Ge Feng ◽  
Xiaoqiang Li ◽  
Xiaobing Wu
Keyword(s):  
Phylogenetic Analyses ◽  
Sister Group ◽  
Molecular Data ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Nucleotide Level ◽  
Protein Coding ◽  
Genome Features ◽  
Gavialis Gangeticus ◽  
Complete Mitochondrial Genomes

AbstractThe complete mitochondrial (mt) genomes of two crocodilians: Crocodylus palustris and Crocodylus mindorensis, were sequenced in order to examine their gene and genome features. Additionally, we intended to increase the amount of molecular data suitable for phylogenetic analysis. Their gene orders conform to other crocodilians that have been sequenced, except the arrangement of two tRNA genes differ from other vertebrates, showing that the gene order of crocodilians is remarkably conserved. Phylogenetic analyses (maximum likelihood, Bayesian inference) based on the mt protein-coding genes at the nucleotide level were performed among crocodilians for which complete mt genomes were available. The results suggest that the gharial (Gavialis gangeticus) joins the false gharial (Tomistoma schlegelii) on a common branch, that constitutes a sister group to traditional Crocodylidae. In this report, Mecistops cataphractus is evidently most closely related to Osteolaemus tetraspis. They are isolated as sister taxon from the main clades in Crocodylus. Regarding Paleosuchus, it appears as sister group to Caiman within the Alligatoridae. In particular, relationships among species of Crocodylus (true crocodiles) are discussed.

scholarly journals Characterization and Phylogenetic Implications of the Complete Mitochondrial Genome of Syrphidae

Genes ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 563 ◽  
Author(s):  
Hu Li
Keyword(s):  
Mitochondrial Genome ◽  
Stop Codon ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Future Studies ◽  
Protein Coding Genes ◽  
Phylogenetic Implications ◽  
Paraphyletic Group ◽  
Complete Mitochondrial Genomes

In this study, the complete mitochondrial genomes (mitogenomes) of two hoverfly species of Korinchia angustiabdomena (Huo, Ren, and Zheng) and Volucella nigricans Coquillett (Diptera: Syrphidae) were determined and analyzed. The circular mitogenomes were 16,473 bp in K. angustiabdomena (GenBank No. MK870078) and 15,724 bp in V. nigricans (GenBank No. MK870079). Two newly sequenced mitogenomes both contained 37 genes, and the gene order was similar with other syrphine species. All the protein-coding genes (PCGs) were started with the standard ATN codons; and most of PCGs were terminated with a TAA stop codon, while ND1 in K. angustiabdomena ended with a TAG codon, and ND5 terminated with truncated T stop codons in both species. The phylogenetic relationship between K. angustiabdomena and V. nigricans with related lineages was reconstructed using Bayesian inference and Maximum-likelihood analyses. The monophyly of each family considered within Muscomorpha was confirmed by the clades in the phylogenetic tree, and superfamily of the Oestroidea (Calliphoridae, Sarcophagidae, and Oestridae) was unexpectedly found to be a paraphyletic group based on our selected data. This mitogenome information for K. angustiabdomena and V. nigricans could facilitate future studies of evolutionarily related insects.

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.

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