Mitochondrial genes as strong molecular markers for species identification

Elyasigorji, Zahra; Izadpanah, Mehrnaz; Hadi, Faranak; Zare, Maryam

doi:10.1007/s13237-022-00393-4

Cited by 8 publications

(7 citation statements)

References 132 publications

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“… 2014 ; Elyasigorji et al. 2023 ). In this study, we sequenced the complete mitochondrial genome of Bu.…”

Section: Introductionmentioning

confidence: 99%

Complete mitochondrial genome sequence of Butyriboletus hainanensis (Boletales, Basidiomycota)

Zeng,

Huang,

et al. 2024

Mitochondrial DNA Part B

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Butyriboletus hainanensis , a macrofungus belonging to the Boletaceae family, is named after its collection location on Hainan Island, China. However, little is known about its mitochondrial genome and its phylogenetic relationship with other boletes. In this study, we utilized next-generation sequencing technology to sequence the mitochondrial genome of Bu. hainanensis . Our findings revealed that the mitochondrial genome of this species is presumably a circular DNA molecule spanning 36,592 bp. It consists of 15 protein-coding genes, 27 transfer RNA genes, and two ribosomal RNA genes. The base composition of the mitochondrial genome is as follows: A (36.64%), C (12.22%), G (11.73%), and T (39.41%), with a GC content of 23.95%. Additionally, a phylogenetic tree was constructed based on 22 mitochondrial genomes, which provided valuable insights into the phylogenetic relationships of Bu. hainanensis with other boletes for the first time.

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“… 2014 ; Elyasigorji et al. 2023 ). In this study, we sequenced the complete mitochondrial genome of Bu.…”

Section: Introductionmentioning

confidence: 99%

Complete mitochondrial genome sequence of Butyriboletus hainanensis (Boletales, Basidiomycota)

Zeng,

Huang,

et al. 2024

Mitochondrial DNA Part B

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“…However, ongoing molecular techniques based on real time PCR (RT-PCR) are being claimed for their best sensitivity, specificity, reproducibility and multiplexing facility. Elyasigorji [ 24 ] noted that elusive and poorly identified species by other methods can be investigated in depth by DNA or protein analysis using molecular techniques such as RT-PCR. After the COVID-19 pandemic, RT-PCR was assumed worldwide as the gold standard for the diagnosis of the virus and has effectively contributed to its control.…”

Section: Introductionmentioning

confidence: 99%

Application of real-time PCR for the identification of the endangered species Galemys pyrenaicus through faecal samples

Ripa,

Díaz-Caballero,

Palacios-González

et al. 2024

Mol Biol Rep

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Background Currently, many micromammals are important targets for study. The endangered Galemys pyrenaicus is an outstanding example. Globally, their populations have suffered a substantial decline in last 20 years. In the surveyed area, the capture of desman is legally forbidden due to the high conservation concerns. Reason by non-invasive sampling through faeces is proposed for its monitoring. Furthermore, the confusion between faeces from desman and Mediterranean water shrews must be considered. Thus, the aim of this study was focused on developing RT-PCR assays to determine the presence of Galemys pyrenaicus and N. a. anomalus from non-invasive samples. Methods and results The study was conducted in the mountains of the System Central of Extremadura (Spain). A total of 186 samples were collected from 2018 to 2021 by experts where historically reported and/or our previous studies confirmed their presence. RT-PCR assays using hydrolysis probes were designed to detect genetic material from both desman and Mediterranean water shrews and its specificity was confirmed. The reliability of the method was further assessed by PCR sequencing of mitochondrial Cyb and d-loop, resulting fully compatible with the RT-PCR approach. Intraspecific phylogenetic relationship was reported to improve knowledge about mtDNA variability in the desman from the Central System. Conclusions We demonstrated that RT-PCR gives a gold opportunity to further map the species using faeces which minimizes disturbance and reports both population status and individual presence. Cost-effective RT-PCR combined with field-collected faeces allows us to better investigate the full range of occurrence of the species.

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“…Ancient eDNA (aeDNA) fragments from eukaryotic species, alongside other sediment characteristics, offer a novel method to examine past ecosystems, speciation and extinction timing, as well as population structure and migration dynamics (Dussex et al, 2021; Ficetola et al, 2018; Graham et al, 2016; Jørgensen et al, 2012; Pansu et al, 2015; Pedersen et al, 2016; Zavala et al, 2021). Mitochondrial DNA (mtDNA) is often used in aeDNA analysis for species identification due to its high abundance and smaller genome compared to the nucleus, facilitating quicker species characterisations (Crampton‐Platt et al, 2016; Elyasigorji et al, 2022; Gómez‐Rodrıguez et al, 2015; Murchie, Monteath, et al, 2021; Slon et al, 2017; Zavala et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

euka: Robust tetrapodic and arthropodic taxa detection from modern and ancient environmental DNA using pangenomic reference graphs

Vogel,

Rubin,

Swartz

et al. 2023

Methods Ecol Evol

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Ancient environmental DNA (aeDNA) is a crucial source of information for past environmental reconstruction. However, the computational analysis of aeDNA involves the inherited challenges of ancient DNA (aDNA) and the typical difficulties of eDNA samples, such as taxonomic identification and abundance estimation of identified taxonomic groups. Current methods for aeDNA fall into those that only perform mapping followed by taxonomic identification and those that purport to do abundance estimation. The former leaves abundance estimates to users, while methods for the latter are not designed for large metagenomic datasets and are often imprecise and challenging to use. Here, we introduce euka, a tool designed for rapid and accurate characterisation of aeDNA samples. We use a taxonomy‐based pangenome graph of reference genomes for robustly assigning DNA sequences and use a maximum‐likelihood framework for abundance estimation. At the present time, our database is restricted to mitochondrial genomes of tetrapods and arthropods but can be expanded in future versions. We find euka to outperform current taxonomic profiling tools and their abundance estimates. Crucially, we show that regardless of the filtering threshold set by existing methods, euka demonstrates higher accuracy. Furthermore, our approach is robust to sparse data, which is idiosyncratic of aeDNA, detecting a taxon with an average of 50 reads aligning. We also show that euka is consistent with competing tools on empirical samples. euka's features are fine‐tuned to deal with the challenges of aeDNA, making it a simple‐to‐use, all‐in‐one tool. It is available on GitHub: https://github.com/grenaud/vgan. euka enables researchers to quickly assess and characterise their sample, thus allowing it to be used as a routine screening tool for aeDNA.

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Mitochondrial genes as strong molecular markers for species identification

Cited by 8 publications

References 132 publications

Complete mitochondrial genome sequence of Butyriboletus hainanensis (Boletales, Basidiomycota)

Complete mitochondrial genome sequence of Butyriboletus hainanensis (Boletales, Basidiomycota)

Application of real-time PCR for the identification of the endangered species Galemys pyrenaicus through faecal samples

euka: Robust tetrapodic and arthropodic taxa detection from modern and ancient environmental DNA using pangenomic reference graphs

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