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

Vanhove, Maarten Pieterjan; Briscoe, Andrew G.; Jorissen, Michiel; Littlewood, D. Timothy J.; Huyse, Tine

doi:10.1186/s12864-018-4893-5

Cited by 44 publications

(56 citation statements)

References 108 publications

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“…In this study, we propose a NAD2 fragment as a specific marker for the common pandora. The gene NAD2 was previously investigated as a marker for population studies of plants, parasites and animals [ 22 , 23 , 24 , 25 ]. However, no use is made of this gene, as far as we know, in fish species identification against frauds, and our results show that its use warrants further investigation.…”

Section: Introductionmentioning

confidence: 99%

A Rapid Method for the Identification of Fresh and Processed Pagellus erythrinus Species against Frauds

Ceruso

Mascolo

Luca

et al. 2020

Foods

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The commercialization of porgies or seabreams of the family Sparidae has greatly increased in the last decade, and some valuable species have become subject to seafood substitution. DNA regions currently used for fish species identification in fresh and processed products belong to the mitochondrial (mt) genes cytochrome b (Cytb), cytochrome c oxidase I (COI), 16S and 12S. However, these markers amplify for fragments with lower divergence within and between some species, failing to provide informative barcodes. We adopted comparative mitogenomics, through the analysis of complete mtDNA sequences, as a compatible approach toward studying new barcoding markers. The intent is to develop a specific and rapid assay for the identification of the common pandora Pagellus erythrinus, a sparid species frequently subject to fraudulent replacement. The genetic diversity analysis (Hamming distance, p-genetic distance, gene-by-gene sequence variability) between 16 sparid mtDNA genomes highlighted the discriminating potential of a 291 bp NAD2 gene fragment. A pair of species-specific primers were successfully designed and tested by end-point and real-time PCR, achieving amplification only in P. erythrinus among several fish species. The use of the NAD2 barcoding marker provides a rapid presence/absence method for the identification of P. erythrinus.

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Section: Introductionmentioning

confidence: 99%

A Rapid Method for the Identification of Fresh and Processed Pagellus erythrinus Species against Frauds

Ceruso

Mascolo

Luca

et al. 2020

Foods

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“…For colonial volvocine algae, previous studies have mainly focused on the conformation of mtDNA, and few have reported phylogenetic analyses based on mtDNA protein-coding genes in this group of algae. Phylogeny based on mtDNA has been widely used in different types of species, such as fish, parasites, brown algae, red algae, and green algae [8][9][10][11][12]. The phylogenetic analyses among colonial volvocine algae in previous studies were mainly based on genes such as the internal transcribed spacer (ITS), the large subunit of the ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcL) gene, five chloroplast protein-coding genes, and the chloroplast genome [7,[13][14][15][16][17][18][19][20][21][22][23][24][25].…”

Section: Ofmentioning

confidence: 99%

Phylogenetic Analysis and Substitution Rate Estimation of Colonial Volvocine Algae Based on Mitochondrial Genomes

Xing

et al. 2020

Genes

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We sequenced the mitochondrial genome of six colonial volvocine algae, namely: Pandorina morum, Pandorina colemaniae, Volvulina compacta, Colemanosphaera angeleri, Colemanosphaera charkowiensi, and Yamagishiella unicocca. Previous studies have typically reconstructed the phylogenetic relationship between colonial volvocine algae based on chloroplast or nuclear genes. Here, we explore the validity of phylogenetic analysis based on mitochondrial protein-coding genes. We found phylogenetic incongruence of the genera Yamagishiella and Colemanosphaera. In Yamagishiella, the stochastic error and linkage group formed by the mitochondrial protein-coding genes prevent phylogenetic analyses from reflecting the true relationship. In Colemanosphaera, a different reconstruction approach revealed a different phylogenetic relationship. This incongruence may be because of the influence of biological factors, such as incomplete lineage sorting or horizontal gene transfer. We also analyzed the substitution rates in the mitochondrial and chloroplast genomes between colonial volvocine algae. Our results showed that all volvocine species showed significantly higher substitution rates for the mitochondrial genome compared with the chloroplast genome. The nonsynonymous substitution (dN)/synonymous substitution (dS) ratio is similar in the genomes of both organelles in most volvocine species, suggesting that the two counterparts are under a similar selection pressure. We also identified a few chloroplast protein-coding genes that showed high dN/dS ratios in some species, resulting in a significant dN/dS ratio difference between the mitochondrial and chloroplast genomes.

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“…The technique is potentially efficient for old museum material and ethanol-preserved specimens (Staats et al, 2013;Maddison and Cooper, 2014;Linard et al, 2016;Grandjean et al, 2017). Despite recent efforts to obtain DNA sequences through HTS protocols from museum specimens (McCormack et al, 2017;Dabney et al, 2013;McCormack et al, 2016) and ethanol material (do Amaral et al, 2015;Brabec et al, 2015Brabec et al, , 2016Hartikainen et al, 2016;Vanhove et al, 2018), the potential use of genome skimming for this purpose remains unexplored. There is a variety of suitable HTS sequencing platforms and library options to choose from to use in combination with genome skimming, including PCR-based libraries and PCR-free libraries that are less-error prone but require higher input DNA ( 1µg) (Twyford and Ness, 2017).…”

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confidence: 99%

“…Hence, it is not uncommon to find studies addressing phylogenetic relationships at different levels of divergence-including the interest on detecting cryptic species-based on these markers (von Nickisch-Rosenegk et al, 1999;Zehnder and Mariaux, 1999;Hu et al, 2005;Wickström et al, 2005;Littlewood et al, 2008;Brabec et al, 2016;Vanhove et al, 2018, to cite a few). However, to date HTS provided the means of sequencing the complete mitochondrial genome in reasonable time and at relative low cost.…”

mentioning

confidence: 99%

“…As a result, the number of genome sequences published has increased exponentially during the last decades (Park et al, 2006;Hahn et al, 2013;Tan et al, 2017;do Amaral et al, 2015;Vanhove et al, 2018). With the increase of studies using complete mitogenomes, several authors have recognized the virtues of a greater amount of nucleotide sequence data for inferring robust phylogenies in many taxonomic groups such as mammals (Arnason et al, 2002;Campbell and Lapointe, 2011), birds (Pacheco et al, 2011), insects (Cameron, 2014), and flatworms (Brabec et al, 2015(Brabec et al, , 2016Maldonado et al, 2017;Vanhove et al, 2018). In addition, we can also relate the power of resolution of the mitogenome to its genome-level characteristics such as gene arrangements and the positions of mobile genetic elements, which are good alternatives to resolve deeper phylogenetic questions (Waeschenbach et al, 2012;Guo, 2015;.…”

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confidence: 99%

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Peer Review #2 of "Genome skimming is a low-cost and robust strategy to assemble complete mitochondrial genomes from ethanol preserved specimens in biodiversity studies (v0.1)"

2019

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Global loss of biodiversity is an ongoing process that concerns both local and global authorities. Studies of biodiversity mainly involve traditional methods using morphological characters and molecular protocols. However, conventional methods are a time consuming and resource demanding task. The development of high-throughput sequencing (HTS) techniques has reshaped the way we explore biodiversity and opened a path to new questions and novel empirical approaches. With the emergence of HTS, sequencing the complete mitochondrial genome became more accessible, and the number of genome sequences published has increased exponentially during the last decades. Despite the current state of knowledge about the potential of mitogenomics in phylogenetics, this is still a relatively under-explored area for a multitude of taxonomic groups, especially for those without commercial relevance, non-models organisms and with ancient DNA. Here we take the first step to assemble and annotate the genomes from HTS data using a new protocol of genome skimming which will offer an opportunity to extend the field of mitogenomics to under-studied organisms. We extracted genomic DNA from specimens preserved in ethanol. We used Nextera XT DNA to prepare indexed paired-end libraries since it is a powerful tool for working with diverse samples, requiring a low amount of input DNA. We sequenced the samples in two different Illumina platform (MiSeq or NextSeq 550). We trimmed raw reads, filtered and had their quality tested accordingly. We performed the assembly using a baiting and iterative mapping strategy, and the annotated the putative mitochondrion through a semi-automatic procedure. We applied the contiguity index to access the completeness of each new mitogenome. Our results reveal the efficiency of the proposed method to recover the whole mitogenomes of ancient DNA from non-model organisms even if there are gene rearrangement in the specimens. Our findings suggest the potential of combining the adequate platform and library to the

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

Cited by 44 publications

References 108 publications

A Rapid Method for the Identification of Fresh and Processed Pagellus erythrinus Species against Frauds

A Rapid Method for the Identification of Fresh and Processed Pagellus erythrinus Species against Frauds

Phylogenetic Analysis and Substitution Rate Estimation of Colonial Volvocine Algae Based on Mitochondrial Genomes

Peer Review #2 of "Genome skimming is a low-cost and robust strategy to assemble complete mitochondrial genomes from ethanol preserved specimens in biodiversity studies (v0.1)"

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