A Re-Assessment of Positive Selection on Mitochondrial Genomes of High-Elevation Phrynocephalus Lizards

Atlas, Jared; Fu, Jinzhong

doi:10.1007/s00239-020-09991-9

Cited by 3 publications

(2 citation statements)

References 44 publications

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“…However, the inclusion of errors would artificially inflate (in the case of random insertions/ substitutions) or deflate (in the case of mapping biases towards the bait reference allele) divergence estimates, leading to erroneous inferences of the driving forces of divergence events, for example, climatic shifts, natural disasters, continental drift. Furthermore, as the mitogenome includes protein coding genes, which undergo selective processes (Atlas & Fu, 2021;Pavlova et al, 2017), incorrect reconstruction may also influence selection analyses. Population-level analyses may also be impacted, if sequencing errors and damage patterns are incorporated when using an incorrectly assembled mitogenome as mapping reference for DNA read data from conspecific specimens.…”

Section: Discussionmentioning

confidence: 99%

Iteratively mapping ancient DNA to reconstruct highly divergent mitochondrial genomes: An evaluation of software, parameters and bait reference

Westbury

Lorenzen

2022

Methods Ecol Evol

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1. The ability to obtain ancient DNA (aDNA) from extinct species has greatly improved our ability to study their evolutionary histories. Most aDNA studies focus on mitochondrial DNA for both population-level and species-level insights, due to its relatively high abundance and increased obtainability. Although several approaches are available to assemble mitogenomes, high levels of DNA damage and non-target contaminating DNA make many approaches unsuitable for aDNA. Further complicating matters for most extinct species is the lack of a sufficiently closely related extant relative to act as a reference.2. Iterative mapping can assemble mitogenomes without using a close reference sequence, and has been applied to aDNA from various extinct species. Despite its widespread use, the accuracy of the reconstructed assemblies is yet to be comprehensively assessed. Here, we investigated the influence of (i) mapping software (Burrows-Wheeler Alignment [BWA], MITObim and NOVOplasty), (ii) parameters and (iii) bait reference phylogenetic distance on assembly accuracy using two simulated datasets: spotted hyena and various mammalian bait references; southern cassowary and various avian bait references, and two empirical datasets: extinct cave hyena; two extinct sloth species. Specifically, we assessed the accuracy of results through three parameters: pairwise distance to a reference conspecific mitogenome, number of incorrectly inserted base pairs and total length of the assembly.3. We found large discrepancies in the accuracy of reconstructed assemblies using different mapping software, parameters and bait references. Results also varied depending on the dataset, thereby making broad, generalised conclusions difficult. However, the overall most accurate results were obtained with either BWA using a minimum mapping quality of 20 and relaxed mismatch parameters (-n 0.001 -o 2), or MITObim using a mismatch value of 3 or 5. We also show accuracy could be further improved by combining results from multiple bait references.

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Section: Discussionmentioning

confidence: 99%

Iteratively mapping ancient DNA to reconstruct highly divergent mitochondrial genomes: An evaluation of software, parameters and bait reference

Westbury

Lorenzen

2022

Methods Ecol Evol

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“…climatic shifts, natural disasters, continental drift. Furthermore, as the mitogenome includes protein coding genes, which undergo selective processes (Atlas & Fu, 2021;Pavlova et al, 2017), incorrect reconstruction may also influence selection analyses. Population-level analyses may also be impacted, if sequencing errors and damage patterns are incorporated when using an incorrectly assembled mitogenome as mapping reference for DNA read data from conspecific specimens.…”

Section: Discussionmentioning

confidence: 99%

Reconstructing mitochondrial genomes from ancient DNA through iterative mapping: an evaluation of software, parameters, and bait reference

Westbury

Lorenzen

2021

Preprint

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Within evolutionary biology, mitochondrial genomes (mitogenomes) provide useful insights at both population and species level. Several approaches are available to assemble mitogenomes. However, most are not suitable for divergent, extinct species, due to the requirement of a reference mitogenome from a conspecific or close relative, and relatively high-quality DNA.Iterative mapping can overcome the lack of a close reference sequence, and has been applied to an array of extinct species. Despite its widespread use, the accuracy of the reconstructed assemblies are yet to be comprehensively assessed. Here, we investigated the influence of mapping software (BWA or MITObim), parameters, and bait reference phylogenetic distance on the accuracy of the reconstructed assembly using two simulated datasets: (i) spotted hyena and various mammalian bait references, and (ii) southern cassowary and various avian bait references. Specifically, we assessed the accuracy of results through pairwise distance (PWD) to the reference conspecific mitogenome, number of incorrectly inserted base pairs (bp), and total length of the reconstructed assembly.We found large discrepancies in the accuracy of reconstructed assemblies using different mapping software, parameters, and bait references. PWD to the reference conspecific mitogenome, which reflected the level of incorrect base calls, was consistently higher with BWA than MITObim. The same was observed for the number of incorrectly inserted bp. In contrast, the total sequence length was lower. Overall, the most accurate results were obtained with MITObim using mismatch values of 3 or 5, and the phylogenetically closest bait reference sequence. Accuracy could be further improved by combining results from multiple bait references.We present the first comprehensive investigation of how mapping software, parameters, and bait reference influence mitogenome reconstruction from ancient DNA through iterative mapping. Our study provides information on how mitogenomes are best reconstructed from divergent, short-read data. By obtaining the most accurate reconstruction possible, one can be more confident as to the reliability of downstream analyses, and the evolutionary inferences made from them.

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Oviduct Epithelial Cells Constitute Distinct Lineages from the Ampulla to the Isthmus Related to High-Altitude Adaptation in Yak (Bos grunniens)

Zhang

Cui

wang

et al. 2022

Preprint

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High-altitude adaptation is viewed as a biologically based process during which yaks respond to the harsh condition of coldness and low oxygen. Although high-altitude adaptation has been studied intensively, there is a lack of multi-omics analysis on its physiological mechanism. Therefore, in this study, 10X Genomics single-cell technology were adopted to identify cellular heterogeneity and trajectory differentiation in different parts of the yak oviduct, thus further exploring new cell markers and ligand-receptors. Besides, based on the comparison of oviduct epithelial cells from the ampulla and isthmus between the yak and bovine, genes and pathways related to altitude adaptation were discussed by bulk-seq. Single cell RNA sequencing (scRNA-seq) revealed 14 cell types defined by multiple specific molecular markers, the main cell types are epithelial cells, ciliated cells, secretory cells, basal cells, mesenchymal stem cells, T cells, B cells, monocytes, NK cells, macrophages, and fibroblasts, among which basal cells could be differentiated into secretory cells and ciliated cells. Apart from that, immune cells were the apex products of cell development, while ciliated cells had the characteristics of de-differentiation, and the new ligand-receptors CD74-COPa and CD74-APP were found. In addition, by bulk-seq, it was found that in the ampulla, there were 5149 differential genes (1875 up-regulated genes and 3274 down-regulated genes). YME1L1 was down-regulated significantly, whereas PPIB, PCBD, CYTB, RPL24, RPS5, and UBL5 were up-regulated to a great extent. In the isthmus, there were 6313 differential genes (2146 up-regulated genes and 4167 down-regulated genes). Among them, YME1L1, GSTA4, DNTTIP2, TMCO6, LRBA, and MYH14 were down-regulated obviously, while SNRPD3, CYTB, ADIPOQ, RNH1, PRDX5, DPF1, CRYAB, and PRXL2B were up-regulated dramatically. Through the comparison, it was observed that GSTA4 and YME1L1 were down-regulated, while CYTB was up-regulated in the ampulla and the isthmus. Beyond that, the oxidative phosphorylation pathway was explored. In conclusion, it was demonstrated that ciliated cells were featured with dedifferentiation, and new ligand receptors CD74-COPa and CD74-APP were discovered. Furthermore, GSTA4, YME1L1 and CYTB were main molecules of altitude adaptation, and the oxidative phosphorylation pathway was the key pathway of high-altitude adaptation. This study provides basic data on the heterogeneity and cell trajectory of yak oviduct from the single-cell sequence, and provides the key genes and pathways of yak high-altitude adaptation, as well as the theoretical basis and the data for revealing the low pregnancy rate and genetic breeding of yaks.

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A Re-Assessment of Positive Selection on Mitochondrial Genomes of High-Elevation Phrynocephalus Lizards

Cited by 3 publications

References 44 publications

Iteratively mapping ancient DNA to reconstruct highly divergent mitochondrial genomes: An evaluation of software, parameters and bait reference

Iteratively mapping ancient DNA to reconstruct highly divergent mitochondrial genomes: An evaluation of software, parameters and bait reference

Reconstructing mitochondrial genomes from ancient DNA through iterative mapping: an evaluation of software, parameters, and bait reference

Oviduct Epithelial Cells Constitute Distinct Lineages from the Ampulla to the Isthmus Related to High-Altitude Adaptation in Yak (Bos grunniens)

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