Reconstruction of mitochondrial genomes from raw sequencing data provides insights on the phylogeny of Ixodes ticks and cautions for species misidentification

Abstract Motivation Assays in mitochondrial genomics rely on accurate read mapping and variant calling. However, there are known and unknown nuclear paralogs that have fundamentally different genetic properties than that of the mitochondrial genome. Such paralogs complicate the interpretation of mitochondrial genome data and confound variant calling. Results Remove the Numts! (RtN!) was developed to categorize reads from massively parallel sequencing data not based on the expected properties and sequence identities of paralogous nuclear encoded mitochondrial sequences, but instead using sequence similarity to a large database of publicly available mitochondrial genomes. RtN! removes low-level sequencing noise and mitochondrial paralogs while not impacting variant calling, while competing methods were shown to remove true variants from mitochondrial mixtures. Availability and implementation https://github.com/Ahhgust/RtN Supplementary information Supplementary data are available at Bioinformatics online.

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Next-generation sequencing data used to determine the mitochondrial genomes and a preliminary phylogeny of Verophasmatodea insects

Journal of Asia-Pacific Entomology ◽

10.1016/j.aspen.2017.04.012 ◽

2017 ◽

Vol 20 (2) ◽

pp. 713-719 ◽

Cited By ~ 1

Author(s):

Zhijun Zhou ◽

Bei Guan ◽

Jinyan Chai ◽

Xuting Che

Keyword(s):

Next Generation Sequencing ◽

Next Generation Sequencing Data ◽

Mitochondrial Genomes ◽

Next Generation ◽

Sequencing Data ◽

Generation Sequencing

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The genome of Populus alba x Populus tremula var. glandulosa clone 84K

DNA Research ◽

10.1093/dnares/dsz020 ◽

2019 ◽

Vol 26 (5) ◽

pp. 423-431 ◽

Cited By ~ 6

Author(s):

Deyou Qiu ◽

Shenglong Bai ◽

Jianchao Ma ◽

Lisha Zhang ◽

Fenjuan Shao ◽

...

Keyword(s):

De Novo ◽

Nuclear Genome ◽

Northern China ◽

Mitochondrial Genomes ◽

Populus Alba ◽

Sequencing Data ◽

High Quality ◽

Male Individual ◽

Poplar Hybrid ◽

Ecological Importance

AbstractPoplar 84K (Populus alba x P. tremula var. glandulosa) is a fast-growing poplar hybrid. Originated in South Korea, this hybrid has been extensively cultivated in northern China. Due to the economic and ecological importance of this hybrid and high transformability, we now report the de novo sequencing and assembly of a male individual of poplar 84K using PacBio and Hi-C technologies. The final reference nuclear genome (747.5 Mb) has a contig N50 size of 1.99 Mb and a scaffold N50 size of 19.6 Mb. Complete chloroplast and mitochondrial genomes were also assembled from the sequencing data. Based on similarities to the genomes of P. alba var. pyramidalis and P. tremula, we were able to identify two subgenomes, representing 356 Mb from P. alba (subgenome A) and 354 Mb from P. tremula var. glandulosa (subgenome G). The phased assembly allowed us to detect the transcriptional bias between the two subgenomes, and we found that the subgenome from P. tremula displayed dominant expression in both 84K and another widely used hybrid, P. tremula x P. alba. This high-quality poplar 84K genome will be a valuable resource for poplar breeding and for molecular biology studies.

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The use of transcriptomic next-generation sequencing data to assemble mitochondrial genomes of Ancistrus spp. (Loricariidae)

Gene ◽

10.1016/j.gene.2015.08.059 ◽

2015 ◽

Vol 573 (1) ◽

pp. 171-175 ◽

Cited By ~ 11

Author(s):

Daniel A. Moreira ◽

Carolina Furtado ◽

Thiago E. Parente

Keyword(s):

Next Generation Sequencing ◽

Next Generation Sequencing Data ◽

Mitochondrial Genomes ◽

Next Generation ◽

Sequencing Data ◽

Generation Sequencing

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Inheritance of chloroplast and mitochondrial genomes in cucumber revealed by four reciprocal F1 hybrid combinations

Scientific Reports ◽

10.1038/s41598-021-81988-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Hyun-Seung Park ◽

Won Kyung Lee ◽

Sang-Choon Lee ◽

Hyun Oh Lee ◽

Ho Jun Joh ◽

...

Keyword(s):

Chloroplast Genome ◽

De Novo ◽

Whole Genome Sequencing Data ◽

Mitochondrial Genomes ◽

Sequencing Data ◽

F1 Hybrid ◽

Inheritance Patterns ◽

Chloroplast Genomes ◽

Hybrid Seeds ◽

Parental Lines

AbstractBoth genomes in chloroplasts and mitochondria of plant cell are usually inherited from maternal parent, with rare exceptions. To characterize the inheritance patterns of the organelle genomes in cucumber (Cucumis sativus var. sativus), two inbred lines and their reciprocal F1 hybrids were analyzed using an next generation whole genome sequencing data. Their complete chloroplast genome sequences were de novo assembled, and a single SNP was identified between the parental lines. Two reciprocal F1 hybrids have the same chloroplast genomes with their maternal parents. Meanwhile, 292 polymorphic sites were identified between mitochondrial genomes of the two parental lines, which showed the same genotypes with their paternal parents in the two reciprocal F1 hybrids, without any recombination. The inheritance patterns of the chloroplast and mitochondria genomes were also confirmed in four additional cucumber accessions and their six reciprocal F1 hybrids using molecular markers derived from the identified polymorphic sites. Taken together, our results indicate that the cucumber chloroplast genome is maternally inherited, as is typically observed in other plant species, whereas the large cucumber mitochondrial genome is paternally inherited. The combination of DNA markers derived from the chloroplast and mitochondrial genomes will provide a convenient system for purity test of F1 hybrid seeds in cucumber breeding.

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Mitochondrial haplogroup J associated with higher risk of obesity in the Qatari population

Scientific Reports ◽

10.1038/s41598-020-80040-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Mohammed Dashti ◽

Hussain Alsaleh ◽

Juan L. Rodriguez-Flores ◽

Muthukrishnan Eaaswarkhanth ◽

Fahd Al-Mulla ◽

...

Keyword(s):

Metabolic Disorders ◽

Southern Italy ◽

Mean Value ◽

Mitochondrial Genomes ◽

Sequencing Data ◽

Mitochondrial Haplogroups ◽

Mitochondrial Haplogroup ◽

Whole Exome ◽

Whole Exome Sequencing Data ◽

The Mean

AbstractObesity, a major risk factor for metabolic disorders, is highly prevalent in Qatari population. Maternal transmission of obesity traits can be significant; for example, X haplogroup is known to be associated with lower BMI and body fat mass in Northern Europeans and T haplogroup which is a sister haplogroup of J is known to be associated with obesity in Caucasian subjects from Austria and Southern Italy. We aimed to delineate the mitochondrial haplogroups and variants associated with obesity in Qatari population. Mitochondrial genomes of 864 Qatari individuals were extracted from whole exome sequencing data with an average coverage of 77X. We distributed the participants into 2 sub-cohorts: obese (BMI ≥ 30) and non-obese (BMI < 30); the mean value of BMI from these two groups were 36.5 ± 5.7 and 26.5 ± 2.6, respectively. Mitochondrial haplogroup profiling followed by uni- and multivariant association tests adjusted for covariates were performed. Qatari individuals with mitochondrial haplogroup J had an increased (twofold) risk of obesity (odds ratio [OR] 1.925; 95% CI 1.234–3.002; P = 0.0038; the Bonferroni adjusted P value threshold is 0.0041), whereas the individuals with haplogroup X were at low risk of obesity (OR 0.387; 95% CI 0.175–0.857; P = 0.019). Further, a set of 38 mitochondrial variants were found to be associated (at P ≤ 0.05) with obesity in models adjusted for age, sex and haplogroup.

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The alternative reality of plant mitochondrial DNA

10.1101/564278 ◽

2019 ◽

Cited By ~ 5

Author(s):

Alexander Kozik ◽

Beth A. Rowan ◽

Dean Lavelle ◽

Lidija Berke ◽

M. Eric Schranz ◽

...

Keyword(s):

Mitochondrial Dna ◽

Genome Structure ◽

Structural Diversity ◽

Data Availability ◽

Mitochondrial Genomes ◽

Physical Analysis ◽

Sequencing Data ◽

True Nature ◽

Plant Mitochondrial Dna ◽

Long Read

ABSTRACTPlant mitochondrial genomes are usually assembled and displayed as circular maps based on the widely-held assumption that circular genome molecules are the primary form of mitochondrial DNA, despite evidence to the contrary. Many plant mitochondrial genomes have one or more pairs of large repeats that can act as sites for inter- or intramolecular recombination, leading to multiple alternative genomic arrangements (isoforms). Most mitochondrial genomes have been assembled using methods that were unable to capture the complete spectrum of isoforms within a species, leading to an incomplete inference of their structure and recombinational activity. To document and investigate underlying reasons for structural diversity in plant mitochondrial DNA, we used long-read (PacBio) and short-read (Illumina) sequencing data to assemble and compare mitochondrial genomes of domesticated (Lactuca sativa) and wild (L. saligna and L. serriola) lettuce species. This allowed us to characterize a comprehensive, complex set of isoforms within each species and to compare genome structures between species. Physical analysis of L. sativa mtDNA molecules by fluorescence microscopy revealed a variety of linear, branched linear, and circular structures. The mitochondrial genomes for L. sativa and L. serriola were identical in sequence and arrangement, and differed substantially from L. saligna, indicating that the mitochondrial genome structure did not change during domestication. From the isoforms evident in our data, we inferred that recombination occurs at repeats of all sizes at variable frequencies. The differences in genome structure between L. saligna and the two other lettuce species can be largely explained by rare recombination events that rearrange the structure. Our data demonstrate that representations of plant mitochondrial DNA as simple, genome-sized circular molecules are not accurate descriptions of their true nature and that in reality plant mitochondrial DNA is a complex, dynamic mixture of forms.Data AvailabilityBioProject: Organellar genomes of cultivated and wild lettuce (Lactuca) varieties PRJNA508811 https://www.ncbi.nlm.nih.gov/bioproject/508811 and other accessions as indicated through the text and supplemental data.FundingNSF grant MCB-1413152 to ACC and support from UC Davis to RWM.

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Extraction and annotation of human mitochondrial genomes from 1000 Genomes Whole Exome Sequencing data

BMC Genomics ◽

10.1186/1471-2164-15-s3-s2 ◽

2014 ◽

Vol 15 (Suppl 3) ◽

pp. S2 ◽

Cited By ~ 39

Author(s):

Maria Angela Diroma ◽

Claudia Calabrese ◽

Domenico Simone ◽

Mariangela Santorsola ◽

Francesco Maria Calabrese ◽

...

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

Mitochondrial Genomes ◽

Sequencing Data ◽

Exome Sequencing Data ◽

1000 Genomes ◽

Whole Exome ◽

Whole Exome Sequencing Data

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Sequencing and Reconstructing Helminth Mitochondrial Genomes Directly from Genomic Next-Generation Sequencing Data

Methods in Molecular Biology - Parasite Genomics ◽

10.1007/978-1-0716-1681-9_3 ◽

2021 ◽

pp. 27-40

Author(s):

Nikola Palevich ◽

Paul Haydon Maclean

Keyword(s):

Next Generation Sequencing ◽

Next Generation Sequencing Data ◽

Mitochondrial Genomes ◽

Next Generation ◽

Sequencing Data ◽

Generation Sequencing

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Genetic diversity across the mitochondrial genome of eastern oysters (Crassostrea virginica) in the northern Gulf of Mexico

PeerJ ◽

10.7717/peerj.12205 ◽

2021 ◽

Vol 9 ◽

pp. e12205

Author(s):

Chani R. Rue ◽

Jason D. Selwyn ◽

Patricia M. Cockett ◽

Bryan Gillis ◽

Lauren Gurski ◽

...

Keyword(s):

Mitochondrial Genome ◽

Crassostrea Virginica ◽

Phylogenetic Reconstruction ◽

Eastern Oyster ◽

Mitochondrial Genomes ◽

Sequencing Data ◽

Coding Regions ◽

Historic Data ◽

Genome Assemblies ◽

Modern Era

The eastern oyster, Crassostrea virginica, is divided into four populations along the western North Atlantic, however, the only published mitochondrial genome sequence was assembled using one individual in Delaware. This study aimed to (1) assemble C. virginica mitochondrial genomes from Texas with pooled restriction-site-associated DNA sequencing (ezRAD), (2) evaluate the validity of the mitochondrial genome assemblies including comparison with Sanger sequencing data, and (3) evaluate genetic differentiation both between the Delaware and Texas genomes, as well as among three bays in Texas. The pooled-genome-assembled-genomes (PAGs) from Texas exhibited several characteristics indicating that they were valid, including elevated nucleotide diversity in non-coding and the third position of codons, placement as the sister haplotype of the genome from Delaware in a phylogenetic reconstruction of Crassostrea mitochondrial genomes, and a lack of genetic structure in the ND4 gene among the three Texas bays as was found with Sanger amplicons in samples from the same bays several years prior. In the comparison between the Delaware and Texas genome, 27 of 38 coding regions exhibited variability between the two populations, which were differentiated by 273 mutations, versus 1–13 mutations among the Texas samples. Using the full PAGs, there was no additional evidence for population structure among the three Texas bays. While population genetics is rapidly moving towards larger high-density datasets, studies of mitochondrial DNA (and genomes) can be particularly useful for comparing historic data prior to the modern era of genomics. As such, being able to reliably compile mitochondrial genomes from genomic data can improve the ability to compare results across studies.

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