scholarly journals Reanalysis and Revision of the Complete Mitochondrial Genome of Artemia urmiana Günther, 1899 (Crustacea: Anostraca)

Diversity ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 14
Author(s):  
Alireza Asem ◽  
Amin Eimanifar ◽  
Weidong Li ◽  
Chun-Yang Shen ◽  
Farnaz Mahmoudi Shikhsarmast ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Complete Mitochondrial Genome ◽  
Taxonomic Status ◽  
Nucleotide Composition ◽  
Urmia Lake ◽  
Phylogenetic Studies ◽  
Region Length ◽  
Pooled Samples ◽  
Artemia Urmiana

In the previously published mitochondrial genome sequence of Artemia urmiana (NC_021382 [JQ975176]), the taxonomic status of the examined Artemia had not been determined, due to parthenogenetic populations coexisting with A. urmiana in Urmia Lake. Additionally, NC_021382 [JQ975176] has been obtained with pooled cysts of Artemia (0.25 g cysts consists of 20,000–25,000 cysts), not a single specimen. With regard to coexisting populations in Urmia Lake, and intra- and inter-specific variations in the pooled samples, NC_021382 [JQ975176] cannot be recommended as a valid sequence and any attempt to attribute it to A. urmiana or a parthenogenetic population is unreasonable. With the aid of next-generation sequencing methods, we characterized and assembled a complete mitochondrial genome of A. urmiana with defined taxonomic status. Our results reveal that in the previously published mitogenome (NC_021382 [JQ975176]), tRNA-Phe has been erroneously attributed to the heavy strand but it is encoded in the light strand. There was a major problem in the position of the ND5. It was extended over the tRNA-Phe, which is biologically incorrect. We have also identified a partial nucleotide sequence of 311 bp that was probably erroneously duplicated in the assembly of the control region of NC_021382 [JQ975176], which enlarges the control region length by 16%. This partial sequence could not be recognized in our assembled mitogenome as well as in 48 further examined specimens of A. urmiana. Although, only COX1 and 16S genes have been widely used for phylogenetic studies in Artemia, our findings reveal substantial differences in the nucleotide composition of some other genes (including ATP8, ATP6, ND3, ND6, ND1 and COX3) among Artemia species. It is suggested that these markers should be included in future phylogenetic studies.

The complete mitochondrial genome of the plant bug Nesidiocoris tenuis (Reuter) (Hemiptera: Miridae: Bryocorinae: Dicyphini)

Zootaxa ◽  
2012 ◽  
Vol 3554 (1) ◽  
pp. 30 ◽  
Author(s):  
XUN DAI ◽  
HUAIZHU XUN ◽  
JIAN CHANG ◽  
JIANGUO ZHANG ◽  
BAOWEN HU ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Tandem Repeats ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Sister Group ◽  
Nucleotide Composition ◽  
Start Codon ◽  
Trna Genes ◽  
Nesidiocoris Tenuis

Nesidiocoris tenuis (Reuter) is a zoophytophagous mirid which is considered both as a significant natural enemy and an important pest of crops. The complete mitochondrial genome (mitogenome) of N. tenuis was determined using long PCR and a primer walking sequencing strategy. The genome is 17, 544 bp in length and contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes (lrRNA and srRNA), and a duplicate control region. The gene order of this newly sequenced genome is identical with the ground plan of insects. The nucleotide composition is biased toward adenine and thymine with a high AT content (75.0%). The most frequent codons are ATA, TTA, TTT, and ATT. All the PCGs initiate with the standard start codon ATN. All tRNAs have the classic cloverleaf structures, with the exception of tRNASer(UCG), which lacks the dihydrouridine (DHU) arm. Secondary structures of the two ribosomal RNAs were shown referring to previous models. Variable numbers of tandem repeats were detected in the control region. The phylogenetic analyses shows that N. tenuis is the sister group to Lygus lineolaris (Palisot de Beauvois).

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.

The complete mitochondrial genome of the jumping grasshopper Sinopodisma pieli (Orthoptera: Acrididae) and the phylogenetic analysis of Melanoplinae

Zootaxa ◽  
2017 ◽  
Vol 4363 (4) ◽  
pp. 506
Author(s):  
HUAXUAN LIU ◽  
LIYUN YAN ◽  
GUOFANG JIANG
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Genome ◽  
Ribosomal Rna ◽  
Complete Mitochondrial Genome ◽  
Taxonomic Status ◽  
Polymerase Chain Reaction Method ◽  
Ribosomal Rna Genes ◽  
Start Codon ◽  
Trna Genes ◽  
Rna Genes

In this study, we reported the complete mitochondrial genome (mitogenome) of Sinopodisma pieli by polymerase chain reaction method for the first time, the type species of the genus Sinopodisma. Its mitogenome was a circular DNA molecule of 15,625 bp in length, with 76.0% A+T, and contained 13 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes and one A+T control region. The overall base composition of the S. pieli mitogenome was 42.8% for A, 33.2% for T, 13.5% for C, and 10.5% for G, respectively. All 13 mitochondrial PCGs shared the start codon ATN. Twelve of the PCGs ended with termination codon TAA and TAG, while cytochrome coxidase subunit 1 (COI) utilized an incomplete T as terminator codon. All tRNA genes could be folded into the typical cloverleaf secondary structure, except trnS(AGN) lacking of dihydrouridine arm. The sizes of the large and small ribosomal RNA genes were 1379 bp and 794 bp, respectively. The A+T rich region was 798 bp in length and contained 88.5% AT content. A phylogenetic analysis based on 13 PCGs by using Bayesian inference (BI) and maximum likelihood (ML) revealed that Sinopodisma is not monophyletic group. We think that the name and taxonomic status of S. tsinlingensis are right, and it should not be moved into the genus Pedopodisma. These data will provide important information for a better understanding of the population genetics and species identification for Sinopodisma. 

A new species of the genus Tuberfemurus (Orthoptera: Tetrigoidea: Cladonotinae) with comments on the characters of mitochondrial genome

Zootaxa ◽  
2021 ◽  
Vol 5071 (3) ◽  
pp. 437-446
Author(s):  
MENG-QI WANG ◽  
YAO DENG ◽  
DE-LONG GUAN ◽  
BEN-YONG MAO ◽  
MIAO LI
Keyword(s):  
New Species ◽  
Mitochondrial Genome ◽  
Stop Codon ◽  
Complete Mitochondrial Genome ◽  
Hind Femur ◽  
Start Codon ◽  
Gene Arrangement ◽  
Coding Region ◽  
Phylogenetic Studies ◽  
A New Species

A new species, Tuberfemurus viridulus sp. nov. is described and illustrated with photographs. The new species is similar to T. torulisinotus Deng, 2019, but differs from the latter by broader vertex, invisible frontal costa in profile, distinctly truncate apex of hind pronotal process, and two large triangular projections on lower outer carinae of hind femur. An updated key to species of Tuberfemurus is provided. Simultaneously, the complete mitochondrial genome of Tuberfemurus viridulus sp. nov. is sequenced and analyzed. The total length of the assembled mitogenome is 15,060 bp with 37 typical mitochondrial genes and a non-coding region (A + T-rich region). The order and orientation of the gene arrangement pattern are identical to that of most Tetrigoidea species. All PCGs initiate with the standard start codon of ATN, except ATP6 with GAC and ND1 with TTG; and terminate with the complete stop codon (TAA/TAG) or with an incomplete T- codon. This data could provide the genome information available for Tetrigoidea and facilitate phylogenetic studies of related insects.  

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