Comparative Analyses of the Complete Mitochondrial Genomes of Three Lamprotula (Bivalvia: Unionidae) Species: Insight into the Shortcomings of Mitochondrial DNA for Recently Diverged Species Delimitation

Malacologia ◽  
2020 ◽  
Vol 63 (1) ◽  
pp. 51
Author(s):  
Rui-Wen Wu ◽  
Xiong-Jun Liu ◽  
Shan Ouyang ◽  
Xiao-Ping Wu
Keyword(s):  
Mitochondrial Dna ◽  
Species Delimitation ◽  
Mitochondrial Genomes ◽  
Comparative Analyses ◽  
Insight Into ◽  
Complete Mitochondrial Genomes

Comparative analyses of the complete mitochondrial genomes of Ascaris lumbricoides and Ascaris suum from humans and pigs

Gene ◽  
2012 ◽  
Vol 492 (1) ◽  
pp. 110-116 ◽  
Author(s):  
Guo-Hua Liu ◽  
Chang-Yi Wu ◽  
Hui-Qun Song ◽  
Shu-Jun Wei ◽  
Min-Jun Xu ◽  
...  
Keyword(s):  
Ascaris Lumbricoides ◽  
Ascaris Suum ◽  
Mitochondrial Genomes ◽  
Comparative Analyses ◽  
Complete Mitochondrial Genomes

Comparative analyses of the complete mitochondrial genomes of the two ruminant hookworms Bunostomum trigonocephalum and Bunostomum phlebotomum

Gene ◽  
2014 ◽  
Vol 541 (2) ◽  
pp. 92-100 ◽  
Author(s):  
Jun-Feng Gao ◽  
Quan Zhao ◽  
Guo-Hua Liu ◽  
Yan Zhang ◽  
Ying Zhang ◽  
...  
Keyword(s):  
Mitochondrial Genomes ◽  
Comparative Analyses ◽  
Complete Mitochondrial Genomes

scholarly journals A simple centrifugation protocol leads to a 55-fold mitochondrial DNA enrichment and paves the way for future mitogenomic research

2017 ◽  
Author(s):  
Jan Niklas Macher ◽  
Vera Zizka ◽  
Alexander Martin Weigand ◽  
Florian Leese
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genomes ◽  
Shotgun Metagenomics ◽  
Fold Enrichment ◽  
Speed Up ◽  
Mitochondrial Origin ◽  
Reduced Costs ◽  
Mock Communities ◽  
Centrifugation Protocol ◽  
Complete Mitochondrial Genomes

AbstractDNA (meta)barcoding is used to study biodiversity and is available for standardised assessments. However, it suffers from PCR bias, which can lead to the loss of specific taxa. PCR-free techniques such as shotgun metagenomics are therefore thought to be more suited for biodiversity assessments, but are currently limited by incomplete reference libraries.The technique of ‘mitogenome-skimming’ or ‘mitogenomics’, in which complete mitochondrial genomes are sequenced, is ideal to bridge the techniques of (meta)barcoding and metagenomics. However, without the enrichment of mitochondria, roughly 99 % of all sequencing reads are of non-mitochondrial origin and mostly useless for common applications, e.g. species identification.Here, we present a simple centrifugation protocol that leads to an average 140-fold enrichment of mitochondrial DNA. By sequencing six ‘mock’- communities – comprising the freshwater taxa Corbicula fluminea, Gammarus roeselii and Hydropsyche exocellata each – we recovered whole mitochondrial genomes of these species and the acanthocephalan endoparasite Pomphorhynchus laevis.The presented protocol will greatly speed up building reference libraries for whole mitochondrial genomes, as dozens of species could be sequenced on a single MiSeq run. Subsequently, it will also allow biodiversity assessments using mitogenomics at greatly reduced costs in comparison to mitogenomic approaches without prior enrichment for mitochondria.

scholarly journals Mitogenomes Reveal Multiple Colonization of Mountains by Rattus in Sundaland

2020 ◽  
Author(s):  
Miguel Camacho-Sanchez ◽  
Jennifer A Leonard
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Purifying Selection ◽  
High Elevation ◽  
Mitochondrial Genomes ◽  
Tropical Mountains ◽  
Weak Evidence ◽  
History Of ◽  
Phylogenetic Framework ◽  
Complete Mitochondrial Genomes

Abstract Tropical mountains are cradles of biodiversity and endemism. Sundaland, tropical Southeast Asia, hosts 3 species of Rattus endemic to elevations above 2000 m with an apparent convergence in external morphology: Rattus korinchi and R. hoogerwerfi from Sumatra, and R. baluensis from Borneo. A fourth one, R. tiomanicus, is restricted to lowland elevations across the whole region. The origins of these endemics are little known due to the absence of a robust phylogenetic framework. We use complete mitochondrial genomes from the 3 high altitude Rattus, and several related species to determine their relationships, date divergences, reconstruct their history of colonization, and test for selection on the mitochondrial DNA. We show that mountain colonization happened independently in Borneo (<390 Kya) and Sumatra (~1.38 Mya), likely from lowland lineages. The origin of the Bornean endemic R. baluensis is very recent and its genetic diversity is nested within the diversity of R. tiomanicus. We found weak evidence of positive selection in the high-elevation lineages and attributed the greater nonsynonymous mutations on these branches (specially R. baluensis) to lesser purifying selection having acted on the terminal branches in the phylogeny.

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 Characterization of four mitochondrial genomes of family Neritidae (Gastropoda: Neritimorpha) and insight into its phylogenetic relationships

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jian-tong Feng ◽  
Li-ping Xia ◽  
Cheng-rui Yan ◽  
Jing Miao ◽  
Ying-ying Ye ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Gene Order ◽  
Phylogenetic Relationships ◽  
Evolutionary Relationships ◽  
Mitochondrial Genomes ◽  
Phylogenetic Resolution ◽  
Relaxed Molecular Clock ◽  
Insight Into ◽  
Complete Mitochondrial Genomes

AbstractNeritidae is one of the most diverse families of Neritimorpha and possesses euryhaline properties. Members of this family usually live on tropical and subtropical coasts and are mainly gregarious. The phylogenetic relationships between several subclasses of Gastropoda have been controversial for many years. With an increase in the number of described species of Neritidae, the knowledge of the evolutionary relationships in this family has improved. In the present study, we sequenced four complete mitochondrial genomes from two genera (Clithon and Nerita) and compared them with available complete mitochondrial genomes of Neritidae. Gene order exhibited a highly conserved pattern among three genera in the Neritidae family. Our results improved the phylogenetic resolution within Neritidae, and more comprehensive taxonomic sampling of subclass Neritimorpha was proposed. Furthermore, we reconstructed the divergence among the main lineages of 19 Neritimorpha taxa under an uncorrelated relaxed molecular clock.

Comparative analyses of the three complete mitochondrial genomes from forensic important beetle genus Dermestes with phylogenetic relationships

Gene ◽  
2019 ◽  
Vol 706 ◽  
pp. 146-153 ◽  
Author(s):  
Mustafa Zafer Karagozlu ◽  
Hyung-eun An ◽  
Seong Hwan Park ◽  
Sang Eon Shin ◽  
Chang-Bae Kim
Keyword(s):  
Phylogenetic Relationships ◽  
Mitochondrial Genomes ◽  
Comparative Analyses ◽  
Complete Mitochondrial Genomes
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