scholarly journals The first next-generation sequencing approach to the mitochondrial phylogeny of African monogenean parasites (Platyhelminthes: Gyrodactylidae and Dactylogyridae)

2018 ◽  
Author(s):  
Maarten P.M. Vanhove ◽  
Andrew G. Briscoe ◽  
Michiel W.P. Jorissen ◽  
D. Tim J. Littlewood ◽  
Tine Huyse
Keyword(s):  
Next Generation Sequencing ◽  
Gene Order ◽  
Stop Codon ◽  
Start Codon ◽  
Phylogenetic Position ◽  
Next Generation ◽  
Protein Coding ◽  
Complete Mitogenome ◽  
Generation Sequencing ◽  
Mitochondrial Phylogeny

AbstractBackgroundMonogenean flatworms are the main ectoparasites of fishes. Representatives of the species-rich families Gyrodactylidae and Dactylogyridae, especially those infecting cichlid fishes and clariid catfishes, are important parasites in African aquaculture, even more so due to the massive anthropogenic translocation of their hosts worldwide. Several questions on their evolution, such as the phylogenetic position of Macrogyrodactylus and the highly speciose Gyrodactylus, remain unresolved with available molecular markers. Also, diagnostics and population-level research would benefit from the development of higher-resolution genetic markers. We aim to advance genetic work on African monogeneans by providing mitogenomic data of four species (two each belonging to the Gyrodactylidae and Dactylogyridae), and analysing their gene sequences and gene order from a phylogenetic perspective.ResultsBased on Illumina technology, the first four mitochondrial genomes of African monogeneans were assembled and annotated for the cichlid parasites Gyrodactylus nyanzae, Cichlidogyrus halli, Cichlidogyrus mbirizei (near-complete mitogenome) and the catfish parasite Macrogyrodactylus karibae (near-complete mitogenome). The start codon TTG is new for Gyrodactylus and for the Dactylogyridae, as is the incomplete stop codon TA for the Dactylogyridae. The most variable markers are nad genes and these are under relaxed selection. Especially nad2 is promising for primer development. Gene order was identical for protein-coding genes and differed between the African representatives of these families only in a tRNA gene transposition. A mitochondrial phylogeny based on an alignment of nearly 12,500 bp including 12 protein-coding and two ribosomal RNA genes confirms that the Neotropical oviparous Aglaiogyrodactylus forficulatus takes a sister group position with respect to the other gyrodactylids, rather than the supposedly ‘primitive’ African Macrogyrodactylus. Inclusion of the African Gyrodactylus nyanzae confirms the paraphyly of Gyrodactylus. The position of the African dactylogyrid Cichlidogyrus is unresolved, although gene order suggests it is closely related to marine ancyrocephalines.ConclusionsThe amount of mitogenomic data available for gyrodactylids and dactylogyrids is increased by roughly one-third. Our study underscores the potential of mitochondrial genes and gene order in flatworm phylogenetics, and of next-generation sequencing for marker development for these non-model helminths for which few primers are available while they constitute a risk to tropical aquaculture.

scholarly journals The Mitochondrial Genomes of 18 New Pleurosticti (Coleoptera: Scarabaeidae) Exhibit a Novel trnQ-NCR-trnI-trnM Gene Rearrangement and Clarify Phylogenetic Relationships of Subfamilies within Scarabaeidae

Insects ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1025
Author(s):  
Sam Pedro Galilee Ayivi ◽  
Yao Tong ◽  
Kenneth B. Storey ◽  
Dan-Na Yu ◽  
Jia-Yong Zhang
Keyword(s):  
Next Generation Sequencing ◽  
Gene Order ◽  
Phylogenetic Relationships ◽  
Gene Rearrangement ◽  
Next Generation ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Next Generation Sequencing Ngs ◽  
Mt Genome ◽  
Generation Sequencing

The availability of next-generation sequencing (NGS) in recent years has facilitated a revolution in the availability of mitochondrial (mt) genome sequences. The mt genome is a powerful tool for comparative studies and resolving the phylogenetic relationships among insect lineages. The mt genomes of phytophagous scarabs of the subfamilies Cetoniinae and Dynastinae were under-represented in GenBank. Previous research found that the subfamily Rutelinae was recovered as a paraphyletic group because the few representatives of the subfamily Dynastinae clustered into Rutelinae, but the subfamily position of Dynastinae was still unclear. In the present study, we sequenced 18 mt genomes from Dynastinae and Cetoniinae using next-generation sequencing (NGS) to re-assess the phylogenetic relationships within Scarabaeidae. All sequenced mt genomes contained 37 sets of genes (13 protein-coding genes, 22 tRNAs, and two ribosomal RNAs), with one long control region, but the gene order was not the same between Cetoniinae and Dynastinae species. All mt genomes of Dynastinae species showed the same gene rearrangement of trnQ-NCR-trnI-trnM, whereas all mt genomes of Cetoniinae species showed the ancestral insect gene order of trnI-trnQ-trnM. Phylogenetic analyses (IQ-tree and MrBayes) were conducted using 13 protein-coding genes based on nucleotide and amino acid datasets. In the ML and BI trees, we recovered the monophyly of Rutelinae, Cetoniinae, Dynastinae, and Sericinae, and the non-monophyly of Melolonthinae. Cetoniinae was shown to be a sister clade to (Dynastinae + Rutelinae).

scholarly journals Next-generation sequencing of mixed genomic DNA allows efficient assembly of rearranged mitochondrial genomes inAmolops chunganensisandQuasipaa boulengeri

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2786 ◽  
Author(s):  
Siqi Yuan ◽  
Yun Xia ◽  
Yuchi Zheng ◽  
Xiaomao Zeng
Keyword(s):  
Next Generation Sequencing ◽  
Gene Order ◽  
Illumina Miseq ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Gene Rearrangements ◽  
Next Generation ◽  
Protein Coding ◽  
Alignment Errors ◽  
Generation Sequencing

Recent improvements in next-generation sequencing (NGS) technologies can facilitate the obtainment of mitochondrial genomes. However, it is not clear whether NGS could be effectively used to reconstruct the mitogenome with high gene rearrangement. These high rearrangements would cause amplification failure, and/or assembly and alignment errors. Here, we choose two frogs with rearranged gene order,Amolops chunganensisandQuasipaa boulengeri, to test whether gene rearrangements affect the mitogenome assembly and alignment by using NGS. The mitogenomes with gene rearrangements are sequenced through Illumina MiSeq genomic sequencing and assembled effectively by Trinity v2.1.0 and SOAPdenovo2. Gene order and contents in the mitogenome ofA. chunganensisandQ. boulengeriare typical neobatrachian pattern except for rearrangements at the position of “WANCY” tRNA genes cluster. Further, the mitogenome ofQ. boulengeriis characterized with a tandem duplication oftrnM. Moreover, we utilize 13 protein-coding genes ofA. chunganensis,Q. boulengeriand other neobatrachians to reconstruct the phylogenetic tree for evaluating mitochondrial sequence authenticity ofA. chunganensisandQ. boulengeri. In this work, we provide nearly complete mitochondrial genomes ofA. chunganensisandQ. boulengeri.

scholarly journals Blackcurrant Leaf Chlorosis Associated Virus: Next-Generation Sequencing Reveals an Extraordinary Virus with Multiple Genomic Components Including Evidence of Circular RNA

2018 ◽  
Author(s):  
Delano James ◽  
James Phelan ◽  
Daniel Sanderson
Keyword(s):  
Next Generation Sequencing ◽  
Stop Codon ◽  
Distinct Species ◽  
Circular Rna ◽  
Open Reading Frames ◽  
Start Codon ◽  
Next Generation ◽  
Leaf Chlorosis ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Blackcurrant leaf chlorosis associated virus (BCLCaV) was detected recently by next-generation sequencing (NGS) and proposed as a new and distinct species in the genus Idaeovirus. Genomic components of BCLCaV that were detected and confirmed include: 1) RNA-1 that is monocistronic and encodes the replicase complex; 2) a bicistronic RNA-2 that encodes a movement protein (MP) and the coat protein (CP) of the virus, with open reading frames (ORF) that overlap by a single adenine (A) nucleotide (nt) representing the third position of an opal stop codon of the MP ORF2a and the first position of the start codon of the CP ORF2b; 3) a subgenomic form of RNA-2 (RNA-3) that contains ORF2b; and 4) a concatenated form of RNA-2 that consists of a complementary and inverted RNA-3 conjoined to the full-length RNA-2. Analysis of NGS-derived paired-end reads revealed the existence of bridge reads encompassing the 3’-terminus and 5’-terminus of RNA-2 or RNA-3 of BCLCaV. The full RNA-2 or RNA-3 could be amplified using outward facing or abutting primers; also RNA-2/RNA-3 could be detected even after three consecutive RNase R enzyme treatments with denaturation at 95 oC preceding each digestion. Evidence was obtained indicating that there are circular forms of BCLCaV RNA-2 and RNA-3.

scholarly journals The complete mitogenome of  Lysmata vittata (Crustacea: Decapoda: Hippolytidae) and its phylogenetic position in Decapoda

2021 ◽  
Author(s):  
Longqiang Zhu ◽  
Zhihuang Zhu ◽  
Leiyu Zhu ◽  
Dingquan Wang ◽  
Jianxin Wang ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Stop Codon ◽  
Nucleotide Composition ◽  
Start Codon ◽  
Phylogenetic Position ◽  
Base Pairs ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Complete Mitogenome ◽  
Rna Genes

In this study, the complete mitogenome of Lysmata vittata (Crustacea: Decapoda: Hippolytidae) has been determined. The genome sequence was 22003 base pairs (bp) and it included thirteen protein-coding genes (PCGs), twenty-two transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and three putative control regions (CRs). The nucleotide composition of AT was 71.50%, with a slightly negative AT skewness (-0.04). Usually the standard start codon of the PCGs was ATN, while cox1, nad4L and cox3 began with TTG, TTG and GTG. The canonical termination codon was TAA, while nad5 and nad4 ended with incomplete stop codon T, and cox1 ended with TAG. We compared the order of genes of Decapoda ancestor and found that the positions of the two tRNAs genes ( trnA and trnR ) of the L. vittata were translocated. The phylogenetic tree showed that L. vittata was an independent clade, namely Hippolytidae.

scholarly journals Next generation sequencing yields the complete mitogenome of Smith’s zokor (Eospalax smithii)

2020 ◽  
Vol 5 (3) ◽  
pp. 2109-2110
Author(s):  
Zhenyuan Cai ◽  
Jingjie Zhang ◽  
Penghai Qiao ◽  
Wen Qing ◽  
Tongzuo Zhang
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Complete Mitogenome ◽  
Generation Sequencing

scholarly journals Mitogenomes of nine Asian skipper genera and their phylogenetic position (Lepidoptera: Hesperiidae: Pyrginae)

2021 ◽  
Author(s):  
Jintian Xiao ◽  
Jiaqi Liu ◽  
Lu yao Ma ◽  
Hideyuki Chiba ◽  
Xiangyu Hao ◽  
...  
Keyword(s):  
Stop Codon ◽  
Phylogenetic Signal ◽  
Start Codon ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Trna Genes ◽  
Protein Coding ◽  
The Status ◽  
The One ◽  
Complete Mitochondrial Genomes

In this study, complete mitochondrial genomes of nine species representing three tribes in the subfamily Pyrginae sensu lato were newly sequenced. The mitogenomes are closed double-stranded circular molecules, with the length ranging from 15,232 bp to 15,559 bp, which all encode 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region. The orientation and gene order of these nine mitogenomes are identical to the inferred ancestral arrangement of insects. All PCGs exhibit the typical start codon ATN except for cox1 (using CGA) and cox2 (using TTG) in Mooreana trichoneura. Most of the PCGs terminate with a TAA stop codon, while cox1, cox2, nad4, and nad5 end with the incomplete codon single T. For the different datasets, we found that the one comprising all 37 genes of mitogenome produced the highest nodal support, indicating that the inclusion of RNAs improves the phylogenetic signal. This study re-confirmed the status of Capila, Pseudocoladenia and Sarangesa, namely Capila belongs to the tribe Tagiadini, and Pseudocoladenia and Sarangesa to the tribe Celaenorrhini. Diagnostic characters distinguishing the two tribes, the length of the forewing cell and labial palpi, are no longer significant. Two population of Pseudocoladenia dan fabia from China and Myanmar and P. dan dhyana from Thailand are confirmed conspecific.

scholarly journals Phylogenetic Position of the Genus Alulacris (Orthoptera: Acrididae: Melanoplinae: Podismini) Revealed by Complete Mitogenome Evidence

Insects ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 918
Author(s):  
Haiyang Xu ◽  
Benyong Mao ◽  
Sergey Yu. Storozhenko ◽  
Yuan Huang ◽  
Zhilin Chen ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Phylogenetic Trees ◽  
Morphological Character ◽  
Morphological Characters ◽  
Phylogenetic Position ◽  
High Quality ◽  
Sequencing Cost ◽  
Complete Mitogenome ◽  
Data Source ◽  
Generation Sequencing

Whole mitogenomes are a useful data source for a wide variety of research goals due to the vastly cheaper sequencing cost and the far less demanding high-quality templates. The mitogenome has demonstrated great potential in resolving phylogenetic questions in Orthoptera at different taxonomic scales as well as exploring patterns of molecular and morphological character evolutions. In this study, the complete mitogenome of Alulacris shilinensis (Zheng, 1977) was sequenced using next-generation sequencing, the characteristics of the mitogenome are presented briefly, and the phylogeny of the Melanoplinae and Catantopinae was reconstructed using a selected dataset of mitogenome sequences under maximum likelihood and Bayesian inference frameworks. The results show that the genus was consistently assigned to the subfamily Melanoplinae rather than Catantopinae in all phylogenetic trees deduced from different datasets under different frameworks, and this finding is entirely consistent with its morphological characters. Therefore, it is more appropriate to place the genus Alulacris in Melanoplinae rather than in Catantopinae.

scholarly journals Next-generation sequencing yields the complete mitogenome of Favia favus

2019 ◽  
Vol 4 (1) ◽  
pp. 1543-1544
Author(s):  
Fei Tong ◽  
Wen Jing Chen ◽  
Pi Mao Chen ◽  
Lu Zhang
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Complete Mitogenome ◽  
Generation Sequencing
Sign in / Sign up

Export Citation Format

Share Document