scholarly journals Characterization and Analysis of the Mitochondrial Genome of Common Bean (Phaseolus vulgaris) by Comparative Genomic Approaches

2020 ◽  
Vol 21 (11) ◽  
pp. 3778
Author(s):  
Changwei Bi ◽  
Na Lu ◽  
Yiqing Xu ◽  
Chunpeng He ◽  
Zuhong Lu
Keyword(s):  
Phaseolus Vulgaris ◽  
Mitochondrial Genome ◽  
Common Bean ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Comparative Genomic ◽  
Trna Genes ◽  
Leguminous Plants ◽  
The Common

The common bean (Phaseolus vulgaris) is a major source of protein and essential nutrients for humans. To explore the genetic diversity and phylogenetic relationships of P. vulgaris, its complete mitochondrial genome (mitogenome) was sequenced and assembled. The mitogenome is 395,516 bp in length, including 31 unique protein-coding genes (PCGs), 15 transfer RNA (tRNA) genes, and 3 ribosomal RNA (rRNA) genes. Among the 31 PCGs, four genes (mttB, nad1, nad4L, and rps10) use ACG as initiation codons, which are altered to standard initiation codons by RNA editing. In addition, the termination codon CGA in the ccmFC gene is converted to UGA. Selective pressure analysis indicates that the ccmB, ccmFC, rps1, rps10, and rps14 genes were under evolutionary positive selection. The proportions of five amino acids (Phe, Leu, Pro, Arg, and Ser) in the whole amino acid profile of the proteins in each mitogenome can be used to distinguish angiosperms from gymnosperms. Phylogenetic analyses show that P. vulgaris is evolutionarily closer to the Glycininae than other leguminous plants. The results of the present study not only provide an important opportunity to conduct further genomic breeding studies in the common bean, they also provide valuable information for future evolutionary and molecular studies of leguminous plants.

scholarly journals Complete mitochondrial genome of Whitmania laevis (Annelida, Hirudinea) and comparative analyses within Whitmania mitochondrial genomes

2020 ◽  
Vol 145 (2) ◽  
Author(s):  
Fei Ye ◽  
Ting Liu ◽  
Wenbo Zhu ◽  
Ping You
Keyword(s):  
Mitochondrial Genome ◽  
Ribosomal Rna ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Rrna Genes ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Protein Coding ◽  
Close Relationship

The complete mitochondrial genome of Whitmania laevis is 14,442 bp in length and contains 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes. The almost-complete mitochondrial genome of Whitmania acranulata, consisting of 13,494 bp, contains 35 genes including 13 PCGs, 20 tRNA genes, and two rRNA genes. COI phylogenetic analyses showed that the samples reported in GenBank and analysed as Hirudo nipponia KC667144, Hirudinaria manillensis KC688268 and Erpobdella octoculata KC688270 are not the named species and they should belong to Whitmania. We compared and analyzed the characteristics of nucleotide composition, codon usage, and secondary structures of 22 tRNAs and two rRNAs from Whitmania taxa. Moreover, we analyzed phylogenetic relationships of Annelida using maximum likelihood (ML) and Bayesian inference (BI) methods, based on 11 mitochondrial genes. Our results reveal that W. laevis has a close relationship with W. pigra.

The complete mitochondrial genome of the storage mite pest Tyrophagus fanetzhangorum (Acari: Acaridae)

2020 ◽  
Vol 25 (9) ◽  
pp. 1693-1701
Author(s):  
Xuan Su ◽  
Yu Fang ◽  
Jiao-Yang Xu ◽  
Wei-Xi Fang ◽  
Xue-Bing Zhan ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Ribosomal Rna ◽  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Gene Arrangement ◽  
Trna Genes ◽  
Storage Mite ◽  
Astigmatid Mites

Mitochondrial (mt) genomes of astigmatid mites typically contain 37 genes for 13 proteins, two ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes. However, two Tyrophagus mites (Tyrophagus putrescentiae and T. longior) were reported as having lost three tRNAs in their mt genomes. In this study, we sequenced the complete mitochondrial genome of Tyrophagus fanetzhangorum (14,257 bp) and found typical set of mt tRNA genes (22 tRNAs). The gene arrangement of T. fanetzhangorum is consistent with the pattern of possible common ancestor of astigmatid mites. Phylogenetic analyses were conducted using Maximum likelihood (ML) and Bayesian inference (BI) methods. Phylogenetic analysis shows that T. fanetzhangorum is more closely related to T. putrescentiae than to T. longior within the genus Tyrophagus.

scholarly journals The first complete mitochondrial genome of Cheyletus malaccensis (Acari: Cheyletidae): gene rearrangement

2020 ◽  
Vol 25 (8) ◽  
pp. 1433-1443
Author(s):  
Yang-ming Lan ◽  
Shi-qian Feng ◽  
Li-yuan Xia ◽  
Zhi-hong Li ◽  
Yang Cao ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Mite Species ◽  
Rrna Genes ◽  
Morphological Identification ◽  
Trna Genes ◽  
Protein Coding ◽  
Food Commodities ◽  
Cheyletus Malaccensis

The predatory mite Cheyletus malaccensis (Acari: Cheyletidae), commonly occurring in stores of various food commodities, is an important natural enemy of stored product pests. Disentangling the mt genome sequence of C. malaccensis at molecular level can decrease uncertainties during morphological identification and is useful in reconstructing the phylogeny of Acariformes group. In this study, the complete mitogenome of C. malaccensis was sequenced by the next-generation sequencing. After assembly and annotation, we found the circular 14,732 bp mitogenome of C. malaccensis, containing 13 protein coding genes, 2 ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes. Compared with the ancestral mitogenome organization of arthropods, most of tRNA were truncated without D-arm or/and TψC-arm. Rearrangement was found in 12 mitogenome genes. Phylogenetic analyses based on the mitogenome data from other 29 mite species were inferred by Bayesian and maximum likelihood methods, which strongly supported the closer relationship between C. malaccensis and Tetranychidae than other mites. The obtained results represent the first complete mitochondrial genome record for Cheyletidae group. It may help improve molecular phylogenetic relationship and population genetics of the Cheyletidae.

The complete mitochondrial genome of the Formosan black bear (Ursus thibetanus formosanus)

Zootaxa ◽  
2009 ◽  
Vol 1971 (1) ◽  
pp. 50-58 ◽  
Author(s):  
CHI-LI TSAI ◽  
YII-CHENG CHOU ◽  
CHIH-CHIN SHIH ◽  
HSI-CHI CHENG ◽  
CHIEH-CHUNG YANG ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Pcr Amplification ◽  
Black Bear ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Ursus Thibetanus ◽  
Protein Coding Genes

A complete mitochondrial genome of the Formosan black bear (Ursus thibetanus formosanus) was obtained by PCR amplification and DNA sequencing. The genome spans 17,044 bp that includes 13 protein-coding genes, 22 tRNA genes, and two rRNA genes. The base composition of the heavy strain is 31.0% A, 25.6% C, 15.7% G, and 27.7% T. The control region (CR) is located between tRNA-Pro and tRNA-Phe, consists of 1,595 bp, and comprises 9.4% of the whole genome. The DNA sequence shares 98.7%, 96.3%, 91.0%, 91.8%, and 91.7% similarity with those of U. t. thibetanus, U. t. mupinensis, U. americanus, U. arctos, and U. maritimus respectively. Phylogenetic analyses suggest that the Formosan black bear is more closely related to U. t. thibetanus than to U. t. mupinensis.

scholarly journals The mitochondrial genome of the semi-slug Omalonyx unguis (Gastropoda: Succineidae) and the phylogenetic relationships within Stylommatophora

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0253724
Author(s):  
Leila Belén Guzmán ◽  
Roberto Eugenio Vogler ◽  
Ariel Aníbal Beltramino
Keyword(s):  
Secondary Structure ◽  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Amino Acid Sequences ◽  
Rrna Genes ◽  
Gene Arrangement ◽  
12S Rrna ◽  
Trna Genes ◽  
Secondary Structure Models

Here we report the first complete mitochondrial genome of the semi-slug Omalonyx unguis (d’Orbigny, 1836) (Gastropoda: Succineidae). Sequencing was performed on a specimen from Argentina. Assembly was performed using Sanger data and Illumina next generation sequencing (NGS). The mitogenome was 13,984 bp in length and encoded the 37 typical Metazoan genes. A potential origin for mitochondrial DNA replication was found in a non-coding intergenic spacer (49 bp) located between cox3 and tRNA-Ile genes, and its secondary structure was characterized. Secondary structure models of the tRNA genes of O. unguis largely agreed with those proposed for other mollusks. Secondary structure models for the two rRNA genes were also obtained. To our knowledge, the 12S-rRNA model derived here is the first complete one available for mollusks. Phylogenetic analyses based on the mitogenomes of O. unguis and 37 other species of Stylommatophora were performed using amino acid sequences from the 13 protein-coding genes. Our results located Succineoidea as a sister group of Helicoidea + Urocoptoidea, similar to previous studies based on mitochondrial genomes. The gene arrangement of O. unguis was identical to that reported for another species of Succineoidea. The unique rearrangements observed for this group within Stylommatophora, may constitute synapomorphies for the superfamily.

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 sequence of Labriocimbex sinicus, a new genus and new species of Cimbicidae (Hymenoptera) from China

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7853 ◽  
Author(s):  
Yuchen Yan ◽  
Gengyun Niu ◽  
Yaoyao Zhang ◽  
Qianying Ren ◽  
Shiyu Du ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
New Genus ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Sister Group ◽  
Morphological Characters ◽  
Trna Genes ◽  
Sequencing Data ◽  
Link Type

Labriocimbex sinicus Yan & Wei gen. et sp. nov. of Cimbicidae is described. The new genus is similar to Praia Andre and Trichiosoma Leach. A key to extant Holarctic genera of Cimbicinae is provided. To identify the phylogenetic placement of Cimbicidae, the mitochondrial genome of L. sinicus was annotated and characterized using high-throughput sequencing data. The complete mitochondrial genome of L. sinicus was obtained with a length of 15,405 bp (GenBank: MH136623; SRA: SRR8270383) and a typical set of 37 genes (22 tRNAs, 13 PCGs, and two rRNAs). The results demonstrated that all PCGs were initiated by ATN codon, and ended with TAA or T stop codons. The study reveals that all tRNA genes have a typical clover-leaf secondary structure, except for trnS1. Remarkably, the secondary structures of the rrnS and rrnL of L. sinicus were much different from those of Corynis lateralis. Phylogenetic analyses verified the monophyly and positions of the three Cimbicidae species within the superfamily Tenthredinoidea and demonstrated a relationship as (Tenthredinidae + Cimbicidae) + (Argidae + Pergidae) with strong nodal supports. Furthermore, we found that the generic relationships of Cimbicidae revealed by the phylogenetic analyses based on COI genes agree quite closely with the systematic arrangement of the genera based on the morphological characters. Phylogenetic tree based on two methods shows that L. sinicus is the sister group of Praia with high support values. We suggest that Labriocimbex belongs to the tribe Trichiosomini of Cimbicinae based on adult morphology and molecular data. Besides, we suggest to promote the subgenus Asitrichiosoma to be a valid genus.

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

PLoS ONE ◽  
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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