Museum genomics reveals the Xerces blue butterfly (
            Glaucopsyche xerces
            ) was a distinct species driven to extinction

The last Xerces blue butterfly was seen in the early 1940s, and its extinction is credited to human urban development. This butterfly has become a North American icon for insect conservation, but some have questioned whether it was truly a distinct species, or simply an isolated population of another living species. To address this question, we leveraged next-generation sequencing using a 93-year-old museum specimen. We applied a genome skimming strategy that aimed for the organellar genome and high-copy fractions of the nuclear genome by a shallow sequencing approach. From these data, we were able to recover over 200 million nucleotides, which assembled into several phylogenetically informative markers and the near-complete mitochondrial genome. From our phylogenetic analyses and haplotype network analysis we conclude that the Xerces blue butterfly was a distinct species driven to extinction.

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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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The complete mitochondrial genome of Gyps coprotheres (Aves, Accipitridae, Accipitriformes): phylogenetic analysis of mitogenome among raptors

PeerJ ◽

10.7717/peerj.10034 ◽

2020 ◽

Vol 8 ◽

pp. e10034

Author(s):

Emmanuel Oluwasegun Adawaren ◽

Morne Du Plessis ◽

Essa Suleman ◽

Duodane Kindler ◽

Almero O. Oosthuizen ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Trees ◽

Complete Mitochondrial Genome ◽

Evolutionary Relationship ◽

Species Sensitivity ◽

Model Species ◽

Cathartes Aura ◽

Old World ◽

A Genome ◽

Generation Sequencing

Three species of Old World vultures on the Asian peninsula are slowly recovering from the lethal consequences of diclofenac. At present the reason for species sensitivity to diclofenac is unknown. Furthermore, it has since been demonstrated that other Old World vultures like the Cape (Gyps coprotheres; CGV) and griffon (G. fulvus) vultures are also susceptible to diclofenac toxicity. Oddly, the New World Turkey vulture (Cathartes aura) and pied crow (Corvus albus) are not susceptible to diclofenac toxicity. As a result of the latter, we postulate an evolutionary link to toxicity. As a first step in understanding the susceptibility to diclofenac toxicity, we use the CGV as a model species for phylogenetic evaluations, by comparing the relatedness of various raptor species known to be susceptible, non-susceptible and suspected by their relationship to the Cape vulture mitogenome. This was achieved by next generation sequencing and assembly. The Cape vulture mitogenome had a genome size of 16,908 bp. The mitogenome phylogenetic analysis indicated a close evolutionary relationship between Old World vultures and other members of the Accipitridae as indicated by bootstrap value of 100% on the phylogenetic trees. Based on this, we postulate that the other species could also be sensitive to the toxic effects of diclofenac. This warrants further investigations.

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The complete mitochondrial genome of Xizicus (Haploxizicus) maculatus revealed by Next-Generation Sequencing and phylogenetic implication (Orthoptera, Meconematinae)

ZooKeys ◽

10.3897/zookeys.773.24156 ◽

2018 ◽

Vol 773 ◽

pp. 57-67 ◽

Cited By ~ 5

Author(s):

Mao Shaoli ◽

Yuan Hao ◽

Lu Chao ◽

Zhou Yafu ◽

Shi Fuming ◽

...

Keyword(s):

Next Generation Sequencing ◽

Mitochondrial Genome ◽

Base Composition ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Gene Arrangement ◽

Next Generation ◽

Protein Coding ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Xizicus Gorochov, 1993, the quiet-calling katydid, is a diverse genus with 68 species in world, which includes more than 45 species in China, has undergone numerous taxonomic revisions with contradicting conclusions. In this study the complete mitochondrial genome of Xizicus (Haploxizicus) maculatus collected from Hainan for the first time was sequenced using the Next-Generation Sequencing (NGS) technology. The length of whole mitogenome is 16,358 bp and contains the typical gene arrangement, base composition, and codon usage found in other related species. The overall base composition of the mitochondrial genome is 37.0 % A, 32.2 % T, 20.2 % C, and 10.6 % G. All 13 protein-coding genes (PCGs) began with typical ATN initiation codon. Nine of the 13 PCGs have a complete termination codon, but the remaining four genes (COI, COIII, ND5, and ND4) terminate with an incomplete T. Phylogenetic analyses are carried out based on the concatenated dataset of 13 PCGs and two rRNAs of Tettigoniidae species available in GenBank. Both Bayesian inference and Maximum Likelihood analyses recovered each subfamily as a monophyletic group. Regardless of the position of Lipotactinae, the relationships among the subfamilies of Tettigoniidae were as follows: ((((Tettigoniinae, Bradyporinae) Meconematinae) Conocephalinae) Hexacentrinae). The topological structure of the phylogeny trees showed that the Xizicus (Haploxizicus) maculatus is closer to Xizicus (Xizicus) fascipes than Xizicus (Eoxizicus) howardi.

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The mitochondrial genome of Apion squamigerum (Coleoptera, Curculionoidea, Brentidae) and the phylogenetic implications

PeerJ ◽

10.7717/peerj.8386 ◽

2020 ◽

Vol 8 ◽

pp. e8386 ◽

Cited By ~ 1

Author(s):

Nan Song ◽

Xinxin Li ◽

Xinming Yin ◽

Xinghao Li ◽

Shengjun Yin ◽

...

Keyword(s):

Mitochondrial Genome ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Intergenic Spacer ◽

Sister Group ◽

Phylogenetic Reconstructions ◽

Phylogenetic Implications ◽

Using Data ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

In this article, we present the nearly complete mitochondrial genome (mitogenome) of the weevil beetle Apion squamigerum (Curculionoidea, Brentidae), assembled using data from Illumina next generation sequencing (NGS). This mitogenome was found to be very large, with the total length of 18,562 bp. Two trnM genes were identified. A large non-coding intergenic spacer spanning 1,949 bp occurred between trnI and trnM2. Combined with 111 existing weevil mitogenomes, we conducted phylogenetic reconstructions based on various datasets under maximum likelihood and Bayesian inference. Firstly, phylogenetic analyses robustly supported a sister group of A. squamigerum and Rhopalapion longirostre, namely, that two species of Apioninae (Brentidae) formed a clade. Within the entire Curculionoidea, the Nemonychidae diverged firstly, following the families Anthribidae and Attelabidae. In addition, a large clade comprising the sister families Brentidae and Curculionidae was strongly supported in all trees.

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Genetic Diversity of Enteric Viruses in Children under Five Years Old in Gabon

Viruses ◽

10.3390/v13040545 ◽

2021 ◽

Vol 13 (4) ◽

pp. 545

Author(s):

Gédéon Prince Manouana ◽

Paul Alvyn Nguema-Moure ◽

Mirabeau Mbong Ngwese ◽

C.-Thomas Bock ◽

Peter G. Kremsner ◽

...

Keyword(s):

Genetic Diversity ◽

Preventive Measures ◽

Phylogenetic Analyses ◽

Enteric Viruses ◽

Study Cohort ◽

Viral Agent ◽

A Genome ◽

Stool Samples ◽

Pcr Techniques ◽

High Diversity

Enteric viruses are the leading cause of diarrhea in children globally. Identifying viral agents and understanding their genetic diversity could help to develop effective preventive measures. This study aimed to determine the detection rate and genetic diversity of four enteric viruses in Gabonese children aged below five years. Stool samples from children <5 years with (n = 177) and without (n = 67) diarrhea were collected from April 2018 to November 2019. Norovirus, astrovirus, sapovirus, and aichivirus A were identified using PCR techniques followed by sequencing and phylogenetic analyses. At least one viral agent was identified in 23.2% and 14.9% of the symptomatic and asymptomatic participants, respectively. Norovirus (14.7%) and astrovirus (7.3%) were the most prevalent in children with diarrhea, whereas in the healthy group norovirus (9%) followed by the first reported aichivirus A in Gabon (6%) were predominant. The predominant norovirus genogroup was GII, consisting mostly of genotype GII.P31-GII.4 Sydney. Phylogenetic analysis of the 3CD region of the aichivirus A genome revealed the presence of two genotypes (A and C) in the study cohort. Astrovirus and sapovirus showed a high diversity, with five different astrovirus genotypes and four sapovirus genotypes, respectively. Our findings give new insights into the circulation and genetic diversity of enteric viruses in Gabonese children.

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Next-generation sequencing yields complete mitochondrial genome assembly of peaceful betta fish, Betta imbellis (Teleostei: Osphronemidae)

Mitochondrial DNA Part B ◽

10.1080/23802359.2020.1841582 ◽

2020 ◽

Vol 5 (4) ◽

pp. 3856-3858

Author(s):

Syed Farhan Ahmad ◽

Nararat Laopichienpong ◽

Worapong Singchat ◽

Aorarat Suntronpong ◽

Tavun Pongsanarm ◽

...

Keyword(s):

Next Generation Sequencing ◽

Mitochondrial Genome ◽

Genome Assembly ◽

Complete Mitochondrial Genome ◽

Next Generation ◽

Generation Sequencing

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Complete mitochondrial genome of Black Drongo Dicrurus macrocercus (Passeriformes: Dicruridae) and phylogenetic analyses

Mitochondrial DNA Part B ◽

10.1080/23802359.2021.1920490 ◽

2021 ◽

Vol 6 (8) ◽

pp. 2442-2444

Author(s):

Haibo Zhang ◽

Xue Gou ◽

Shize Li ◽

Cheng Wang ◽

Caichun Peng ◽

...

Keyword(s):

Mitochondrial Genome ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome

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The first mitochondrial genome of the genus Exhippolysmata (Decapoda: Caridea: Lysmatidae), with gene rearrangements and phylogenetic associations in Caridea

Scientific Reports ◽

10.1038/s41598-021-93946-7 ◽

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.

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