Unraveling heteroplasmy patterns with NOVOPlasty

Abstract Heteroplasmy, the existence of multiple mitochondrial haplotypes within an individual, has been studied across different scientific fields. Mitochondrial genome polymorphisms have been linked to multiple severe disorders and are of interest to evolutionary studies and forensic science. Before the development of massive parallel sequencing (MPS), most studies of mitochondrial genome variation were limited to short fragments and to heteroplasmic variants associated with a relatively high frequency (>10%). By utilizing ultra-deep sequencing, it has now become possible to uncover previously undiscovered patterns of intra-individual polymorphisms. Despite these technological advances, it is still challenging to determine the origin of the observed intra-individual polymorphisms. We therefore developed a new method that not only detects intra-individual polymorphisms within mitochondrial and chloroplast genomes more accurately, but also looks for linkage among polymorphic sites by assembling the sequence around each detected polymorphic site. Our benchmark study shows that this method is capable of detecting heteroplasmy more accurately than any method previously available and is the first tool that is able to completely or partially reconstruct the sequence for each mitochondrial haplotype (allele). The method is implemented in our open source software NOVOPlasty that can be downloaded at https://github.com/ndierckx/NOVOPlasty.

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Punctuated plastome reduction and host–parasite horizontal gene transfer in the holoparasitic plant genus Aphyllon

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2018.1535 ◽

2018 ◽

Vol 285 (1887) ◽

pp. 20181535 ◽

Cited By ~ 11

Author(s):

Adam C. Schneider ◽

Harold Chun ◽

Saša Stefanović ◽

Bruce G. Baldwin

Keyword(s):

Mitochondrial Genome ◽

Gene Tree ◽

Recent Common Ancestor ◽

Evolutionary Time ◽

Fine Grained ◽

Plastome Evolution ◽

Chloroplast Genomes ◽

Stem Lineage ◽

Patterns And Processes ◽

Host Parasite

Foundational studies of chloroplast genome (plastome) evolution in parasitic plants have focused on broad trends across large clades, particularly among the Orobanchaceae, a species-rich and ecologically diverse family of root parasites. However, the extent to which such patterns and processes of plastome evolution, such as stepwise gene loss following the complete loss of photosynthesis (shift to holoparasitism), are detectable at shallow evolutionary time scale is largely unknown. We used genome skimming to assemble eight chloroplast genomes representing complete taxonomic sampling of Aphyllon sect. Aphyllon, a small clade within the Orobanchaceae that evolved approximately 6 Ma, long after the origin of holoparasitism. We show substantial plastome reduction occurred in the stem lineage, but subsequent change in plastome size, gene content, and structure has been relatively minimal, albeit detectable. This lends additional fine-grained support to existing models of stepwise plastome reduction in holoparasitic plants. Additionally, we report phylogenetic evidence based on an rbcL gene tree and assembled 60+ kb fragments of the Aphyllon epigalium mitochondrial genome indicating host-to-parasite horizontal gene transfers (hpHGT) of several genes originating from the plastome of an ancient Galium host into the mitochondrial genome of a recent common ancestor of A. epigalium . Ecologically, this evidence of hpHGT suggests that the host–parasite associations between Galium and A. epigalium have been stable at least since its subspecies diverged hundreds of thousands of years ago.

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

Genes ◽

10.3390/genes11010115 ◽

2020 ◽

Vol 11 (1) ◽

pp. 115

Author(s):

Yuxin Hu ◽

Weiyue Xing ◽

Zhengyu Hu ◽

Guoxiang Liu

Keyword(s):

Phylogenetic Analysis ◽

Mitochondrial Genome ◽

Phylogenetic Relationship ◽

Phylogenetic Analyses ◽

Mitochondrial Protein ◽

Substitution Rates ◽

Protein Coding ◽

Protein Coding Genes ◽

Chloroplast Genomes ◽

Volvocine Algae

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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International high-frequency base balance benchmark study

Wind and Structures ◽

10.12989/was.2014.18.4.457 ◽

2014 ◽

Vol 18 (4) ◽

pp. 457-471 ◽

Cited By ~ 9

Author(s):

John D. Holmes ◽

Tim K.T. Tse

Keyword(s):

High Frequency ◽

Benchmark Study ◽

Base Balance

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Effect of prolonged vegetative reproduction of olive tree cultivars (Olea europaea L.) in mitochondrial homoplasmy and heteroplasmy

Genome ◽

10.1139/g03-017 ◽

2003 ◽

Vol 46 (3) ◽

pp. 377-381 ◽

Cited By ~ 15

Author(s):

Angel García-Díaz ◽

Ricardo Oya ◽

Antonio Sánchez ◽

Francisco Luque

Keyword(s):

Mitochondrial Genome ◽

Sexual Reproduction ◽

Olea Europaea ◽

Vegetative Reproduction ◽

Intergenic Spacer Region ◽

Olea Europaea L ◽

Chloroplast Genomes ◽

Mitochondrial Region ◽

Olive Trees ◽

Olea Europaéa

The inheritance of mitochondrial and chloroplast genomes does not follow Mendelian laws, but proceeds by vegetative segregation. Most organisms show organelle homoplasmy, which is probably produced and maintained during sexual reproduction. We have tested the effect of prolonged vegetative multiplication in the maintenance of mitochondrial homoplasmy and the generation of heteroplasmy in cultivated olive trees, Olea europaea L. Seven trees, each representing a different variety of olive, were analysed by the study of an intergenic spacer region of the mitochondrial genome. A very high level of heteroplasmy was detected in all cases. We found multiple genome variants of the sequence analysed. The frequency of genomes with no changes in the spacer region was 11.5%. This means that 88.5% of genomes contain at least one change. The same spacer mitochondrial region was sequenced in several clones from four olive trees of a second generation of sexually reproduced trees. In these trees, many clones were identical and had no changes, which represents a clear reduction of the heteroplasmy (p < 0.001). Therefore, this work supports the relevance of the role of sexual reproduction in the maintenance of mitochondrial homoplasmy and also shows that mutations accumulate in a non-coding sequence of the mitochondrial genome when vegetative propagation is maintained for a long period of time.Key words: mitochondrial genome, homoplasmy, heteroplasmy, olive trees, vegetative reproduction, sexual reproduction.

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Potamopyrgus antipodarum (Gray, 1843) in Polish waters − its mitochondrial haplotype and role as intermediate host for trematodes

Knowledge and Management of Aquatic Ecosystems ◽

10.1051/kmae/2020040 ◽

2020 ◽

pp. 48

Author(s):

Anna Stanicka ◽

Kamila Stefania Zając ◽

Dorota Lachowska-Cierlik ◽

Anna Cichy ◽

Janusz Żbikowski ◽

...

Keyword(s):

Intermediate Host ◽

Potamopyrgus Antipodarum ◽

Mitochondrial Haplotype ◽

Main Role ◽

Larval Stages ◽

Mitochondrial Haplotypes ◽

Second Intermediate Host ◽

Haplotype 1 ◽

New Zealand Mud Snail

The New Zealand mud snail (Potamopyrgus antipodarum (Gray, 1843)) is on the list of one hundred worst invasive species. Researchers point out that genetic variation between populations of P. antipodarum manifested in differences in life-history traits. The main objective of our investigation was to gain pioneer knowledge about mitochondrial haplotypes of P. antipodarum in Polish waters on the background of these haplotypes recorded in the world and confirmation of the main role of P. antipodarum in the life cycle of digenean trematodes. We examined 1000 individuals of P. antipodarum from five water bodies in three different parts of Poland for the presence of larval stages of digenean trematodes. For several randomly selected individuals we carried out DNA sequencing of the 16S ribosomal RNA gene as marker of this non-indigenous mollusk. Only one 16S rRNA haplotype of P. antipodarum was recorded in Polish waters, defined in this study as haplotype 1 which turned out to be the most widespread in Europe. Potamopyrgus antipodarum is a source of trematode metacercariae belonging mainly to the family Echinostomatidae. As a result, we can demonstrate that it plays a role as the second intermediate host of digenean trematodes in European waters.

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Complete Mitochondrial Genomes of Three Mangifera Species, Their Genomic Structure And Gene Transfer From Chloroplast Genomes

10.21203/rs.3.rs-1059761/v1 ◽

2021 ◽

Author(s):

Yingfeng Niu ◽

Chengwen Gao ◽

Jin Liu

Keyword(s):

Mitochondrial Genome ◽

Genomic Structure ◽

Mangifera Indica ◽

Gene Content ◽

Rrna Genes ◽

Mitochondrial Genomes ◽

Trna Genes ◽

Protein Coding ◽

Protein Coding Genes ◽

Chloroplast Genomes

Abstract BackgroundAmong the Mangifera species, mango (Mangifera indica) is an important commercial fruit crop. However, very few studies have been conducted on the Mangifera mitochondrial genome. This study reports and compares the newly sequenced mitochondrial genomes of three Mangifera species. Results Mangifera mitochondrial genomes showed partial similarities in the overall size, genomic structure, and gene content. Specifically, the genomes are circular and contain about 63-69 predicted functional genes, including five ribosomal RNA (rRNA) genes and 24-27 transfer RNA (tRNA) genes. The GC contents of the Mangifera mitochondrial genomes are similar, ranging from 44.42–44.66%. Leucine (Leu) and serine (Ser) are the most frequently used, while tryptophan (Trp) and cysteine (Cys) are the least used amino acids among the protein-coding genes in Mangifera mitochondrial genomes. We also identified 7-10 large chloroplast genomic fragments in the mitochondrial genome, ranging from 1407-6142 bp. Additionally, four intact mitochondrial tRNAs genes (tRNA-Cys, tRNA-Trp, tRNA-Pro, and tRNA-Met) and intergenic spacer regions were identified. Phylogenetic analysis based on the common protein-coding genes of most branches provided a high support value. ConclusionsWe sequenced and compared the mitochondrial genomes of three Mangifera species. The results showed that the gene content of Mangifera mitochondrial genomes is similar across various species. Gene transferred from the chloroplast genome to the mitochondrial genome were identified. This study provides valuable information for evolutionary and molecular studies of Mangifera and a basis for further studies on genomic breeding of mango.

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Mitochondrial relationships between various chamomile accessions

Journal of Applied Genetics ◽

10.1007/s13353-020-00602-3 ◽

2020 ◽

Author(s):

Joana Ruzicka ◽

Marion Hacek ◽

Johannes Novak

Keyword(s):

Mitochondrial Genome ◽

High Resolution Melting ◽

Genetic Distances ◽

Snp Markers ◽

Genotypic Variability ◽

Matricaria Chamomilla ◽

Mitochondrial Haplotypes ◽

Tea Plants ◽

Sample Set ◽

Important Medicinal Plant

AbstractMatricaria chamomilla L. (GRIN; The Plant List 2013) is an important medicinal plant and one of the most frequently consumed tea plants. In order to assess mitochondrial genome variation of different cultivated chamomile accessions, 36 mitochondrial SNP markers were used in a HRM (high resolution melting) approach. In thirteen accessions of chamomile (n = 155), twenty mitochondrial haplotypes (genetic distances 0.028–0.693) were identified. Three of the accessions (‘Camoflora’, ‘Mat19’ and ‘Manzana’) were monomorphic. The highest genotypic variability was found for the Croatian accession ‘PG029’ with nine mitochondrial haplotypes (mitotypes) and the Argentinian ‘Argenmilla’ with seven mitotypes. However, most of the mitotypes detected in these accessions were infrequent in our sample set, thus disclosing an unusual high amount of substitutions within the mitochondrial genome of these accessions. The mitotypes with the highest frequency in the examined dataset were MT1 (n = 27), MT9 (n = 23) and MT17 (n = 20). All of the frequent mitochondrial lines are distributed not only over several accessions but also over several geographical origins. The origins often build a triplet with on average two to three concurrent lines. The most distantly related accessions were ‘Mat19’ and ‘Camoflora’ (0.539), while ‘PNOS’ and ‘Margaritar’ (0.007) showed the lowest genetic distance.

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High Frequency Pulsatile Electromagnetic Fields and Ultrasound Pulsatile Fields Impact on Germination Dynamic at Ocimum basilicum L. and O. basilicum var. purpurascens Benth., Observed with Open Source Software

Notulae Botanicae Horti Agrobotanici Cluj-Napoca ◽

10.15835/nbha44110328 ◽

2016 ◽

Vol 44 (1) ◽

pp. 41-47 ◽

Cited By ~ 1

Author(s):

Ioan ONAC ◽

Valentin SINGUREANU ◽

Gelu MOLDOVAN ◽

Rodica UNGUR

Keyword(s):

Open Source ◽

Seed Development ◽

Electromagnetic Fields ◽

Open Source Software ◽

High Frequency ◽

Low Cost ◽

Native Plant ◽

Hypocotyl Length ◽

Tropical Regions ◽

Vigor Index

Basil (Ocimum sp.), generally knowned as 'king of herbs' due to its pharmaceutical and culinary properties, is considered to be a native plant derived from Africa and Asia. Ocimum sp. grows in tropical and sub-tropical regions with more than 50 species knowned till present time. Germination percent of Ocimum sp. is considered to be between 85-95%. Even though Ocimum sp. are considered to have fast germination velocity index (GVI), short mean germination time (MGT) and increased seedling vigor index (SVI) values, their experimental monitoring is done with specialized software's that are expensive. Low cost scientific solutions are keen on open source software germination protocols. For observing the accuracy of open source C.A.D. software's Ocimum sp. seeds where submitted to high frequency pulsatile electromagnetic fields (300 impulses/3 peak penetrance - 293 W) and ultrasound pulsatile fields (1/2 pulses by 0.5 W/cm2). All sequence images where taken using a positive/negative photo filter enhancing differences in seed development. At the end of the experiment all images where transformed into vector formats (dwg). On the dwg extension, selective free plug-ins such as Face Centroid and Area Properties help to collect data like seed development on X/Y scale, area, perimeter, no. of germinated seeds, length of seedling root, hypocotyl length.

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Arctic charr (Salvelinus alpinus) is a suitable host for Gyrodactylus salaris (Monogenea, Gyrodactylidae) in Norway

Parasitology ◽

10.1017/s0031182006001223 ◽

2006 ◽

Vol 134 (2) ◽

pp. 257-267 ◽

Cited By ~ 26

Author(s):

G. ROBERTSEN ◽

H. HANSEN ◽

L. BACHMANN ◽

T. A. BAKKE

Keyword(s):

Rainbow Trout ◽

Atlantic Salmon ◽

Salvelinus Alpinus ◽

Arctic Charr ◽

First Record ◽

Mitochondrial Haplotype ◽

Stock Management ◽

New Host ◽

Mitochondrial Haplotypes ◽

In The Wild

Gyrodactylus specimens infecting both anadromous Arctic charr (Salvelinus alpinus) from River Signaldalselva (northern Norway) and resident Arctic charr from Lake Pålsbufjorden (southern Norway) were identified as G. salaris using molecular markers and morphometrics. The infection in Pålsbufjorden represents the first record of a viable G. salaris population infecting a host in the wild in the absence of salmon (Salmo salar). G. salaris on charr from Signaldalselva and Pålsbufjorden bear different mitochondrial haplotypes. While parasites infecting charr in Signaldalselva carry the same mitochondrial haplotype as parasites from sympatric Atlantic salmon, G. salaris from charr in Pålsbufjorden bear a haplotype that has previously been found in parasites infecting rainbow trout (Oncorhynchus mykiss) and Atlantic salmon, and an IGS repeat arrangement that is very similar to those observed earlier in parasites infecting rainbow trout. Accordingly, the infection may result from 2 subsequent host-switches (from salmon via rainbow trout to charr). Morphometric analyses revealed significant differences between G. salaris infecting charr in the 2 localities, and between those on sympatric charr and salmon within Signaldalselva. These differences may reflect adaptations to a new host species, different environmental conditions, and/or inherited differences between the G. salaris strains. The discovery of G. salaris on populations of both anadromous and resident charr may have severe implications for Atlantic salmon stock-management as charr may represent a reservoir for infection of salmon.

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Insights into the Mitochondrial and Nuclear Genome Diversity of Two High Yielding Strains of Laying Hens

Animals ◽

10.3390/ani11030825 ◽

2021 ◽

Vol 11 (3) ◽

pp. 825

Author(s):

Clara Heumann-Kiesler ◽

Vera Sommerfeld ◽

Hanna Iffland ◽

Jörn Bennewitz ◽

Markus Rodehutscord ◽

...

Keyword(s):

Mitochondrial Genome ◽

Genetic Background ◽

Laying Hens ◽

Nuclear Genome ◽

Nuclear Interaction ◽

Mitochondrial Haplotype ◽

Essential Components ◽

Different Strains ◽

Eukaryotic Organisms ◽

The Impact

Mitochondria are essential components of eukaryotes as they are involved in several organismic key processes such as energy production, apoptosis and cell growth. Despite their importance for the metabolism and physiology of all eukaryotic organisms, the impact of mitochondrial haplotype variation has only been studied for very few species. In this study we sequenced the mitochondrial genome of 180 individuals from two different strains of laying hens. The resulting haplotypes were combined with performance data such as body weight, feed intake and phosphorus utilization to assess their influence on the hens in five different life stages. After detecting a surprisingly low level of genetic diversity, we investigated the nuclear genetic background to estimate whether the low mitochondrial diversity is representative for the whole genetic background of the strains. Our results highlight the need for more in-depth investigation of the genetic compositions and mito-nuclear interaction in individuals to elucidate the basis of phenotypic performance differences. In addition, we raise the question of how the lack of mitochondrial variation developed, since the mitochondrial genome represents genetic information usually not considered in breeding approaches.

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