Precise annotation of human, chimpanzee, rhesus macaque and mouse mitochondrial genomes using 5’ and 3’ end small RNAs

Yang

et al. 2019

Preprint

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Background: Annotation of mitochondrial (mt) genomes is indispensable for fundamental research in many fields, including mt biochemistry, physiology, and the molecular phylogenetics and evolution of animals. Moreover, high-resolution annotation of animal mt genomes can be used to investigate RNA processing, maturation, degradation, and even the regulation of gene expression. In this study, we used long-PCR amplification combined with Next-Generation Sequencing (NGS) to obtain complete mt genomes of individual ticks and performed precise annotation of these mt genomes. We aimed to: (1) develop a simple, cost-effective and accurate method for the study of extremely high AT-content mt genomes within an individual animal containing miniscule DNA; (2) provide a high-quality reference genome for D. silvarum with precise annotation and also for future studies of other tick mt genomes; and (3) use these mt genomes containing two Control Regions (CRs) to confirm our previous findings from those containing one CR. Results: Based on these mt genome annotations, most of our findings were consistent with those from previous studies. Moreover, two new and important findings were reported for the first time, contributing fundamental knowledge to mt biology. The first was the discovery of a transposon-like element that may eventually reveal much about mechanisms of gene rearrangements in mt genomes. Another finding was that Copy Number Variation (CNV) of Short Tandem Repeats (STRs) account for mitochondrial sequence diversity (heterogeneity) within an individual tick, insect, mouse or human. All the detected DNA variations within a single human cell were CNV of STRs, whereas SNPs were not detected. The CNV of STRs in the protein-coding genes resulted in frameshift mutations in the proteins, which can cause deleterious effects. Mitochondria containing these deleterious STR mutations accumulate in cells and could produce deleterious proteins. Conclusions: We proposed that the accumulation of CNV of STRs in mitochondria causes aging or diseases. Our study will lead to the reconsideration of the importance of STRs and a unified study of CNV of STRs with longer and shorter repeat units (particularly polynucleotides) in both nuclear and mt genomes.

Section: Precise Annotation Of the Dermacentor Silvarum Mt Genomesupporting

confidence: 85%

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Precise annotation of tick mitochondrial genomes reveals multiple copy number variation of short tandem repeats and one transposon-like element

Yang

et al. 2019

Preprint

Self Cite

“…Using these accurate genomes with precise annotations, we discovered that a novel 31-nt ncRNA exists in 97 mammalian mitochondrial DNA [4] and that the copy numbers of tandem repeats exhibit great diversity 98 within an E. fullo individual [5]. Recently, precise annotation of human, chimpanzee, rhesus macaque and 99 mouse mitochondrial genomes has been performed to investigate five Conserved Sequence Blocks (CSBs) 100 in the mitochondrial D-loop region [6], which ultimately led to an understanding of the mechanisms 101 involved in the RNA-DNA transition and even the functions of the D-loop.…”

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confidence: 99%

“…294 The detection of STR variation was reliable, based on the following reasons: (1) the PCR amplification and 295 high-depth DNA sequencing produced a high signal-to-noise ratio in the detection of DNA variation; (2) the 296 Illumina sequencer does not generate InDel errors in the DNA-seq data; (3) the alternative allele ratios 297 (Materials and Methods) at 20 STR positions are significantly higher and the highest ratio reached was 298 ~33% at position 3441 ( Table 3); (4) it was impossible for sequencing or alignment errors to result in 2-bp 299 InDels in 2×n STR (e.g., [TA] 9); (5) the same STR variation caused diversity within and between 300 individuals, e.g., [TA]9 in our genome ( Table 3) and [TA]5 in NC_026552.1; (6) STR variation was detected 301 in other animal species, including E. fullo [5], mouse and human [6]. 302 303 Table 3 Table 3).…”

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Precise annotation of tick mitochondrial genomes reveals multiple STR variation and one transposon-like element

Xu²,

Yang

et al. 2019

Preprint

Self Cite

48In this study, we used long-PCR amplification combined with Next-Generation Sequencing (NGS) to 49 obtain complete mitochondrial genomes of individual ticks and performed precise annotation of these 50 genomes. These annotations were confirmed by the PacBio full-length transcriptome data to cover both 51 entire strands of the mitochondrial genomes without any gaps or overlaps. Based on these annotations, most 52 of our findings were consistent with those from previous studies. Moreover, two important findings were 53 reported for the first time, contributing fundamental knowledge to mitochondrial biology. The first was the 54 discovery of a transposon-like element that may reveal the mechanisms of mitochondrial gene order 55 rearrangement and genomic structural variation. Another finding was that Short Tandem Repeat (STRs) are 56 the dominant variation type causing mitochondrial sequence diversity within an individual tick, insect, 57 mouse and human. Comparisons between interindividual and intraindividual variation showed that 58 polynucleotides and STRs with longer repeat units had the same variation pattern. Particularly, mitochondria 59 containing deleterious mutations can accumulate in cells and deleterious STR mutations irreversibly change 60 the proteins made from their mRNAs. Therefore, we proposed that deleterious STR mutations in 61 mitochondria cause aging and diseases. This finding helped to ultimately reveal the mechanisms of 62 mitochondrial DNA variation and its consequences (e.g., aging and diseases) in animals. Our study will give 63 rise to the reconsideration of the importance of STRs and a unified study of STR variation with longer and 64 shorter repeat units (particularly polynucleotides) in both nuclear and mitochondrial genomes. The complete 65 mitochondrial genome sequence of Dermacentor silvarum is available at the NCBI GenBank database under 66 the accession number MN347015 and the raw data is available at the NCBI SRA database under the 67 accession number SRP178347 . 68 69 70 71 72 73 74 75 76 77 78 79 80

Precise annotation of tick mitochondrial genomes reveals multiple copy number variation of short tandem repeats and one transposon-like element

Xuan

Liang

et al. 2020

Preprint

Self Cite

Background: In the present study, we used long-PCR amplification coupled with Next-Generation Sequencing (NGS) to obtain complete mitochondrial (mt) genomes of individual ticks and unprecedently performed precise annotation of these mt genomes. We aimed to: (1) to develop a simple, cost-effective and accurate method for the study of extremely high AT-content mt genomes within an individual animal containing miniscule DNA (e.g. Dermacentor silvarum); (2) to provide a high-quality reference genome for D. silvarum with precise annotation and also for future studies of other tick mt genomes; and (3) to detect and analyze mt DNA variation within an individual tick.Results: These annotations were confirmed by the PacBio full-length transcriptome data to cover both entire strands of the mitochondrial genomes without any gaps or overlaps. Moreover, two new and important findings were reported for the first time, contributing fundamental knowledge to mt biology. The first was the discovery of a transposon-like element that may eventually reveal much about mechanisms of gene rearrangements in mt genomes. Another finding was that Copy Number Variation (CNV) of Short Tandem Repeats (STRs) account for mitochondrial sequence diversity (heterogeneity) within an individual tick, insect, mouse or human, whereas SNPs were not detected. The CNV of STRs in the protein-coding genes resulted in frameshift mutations in the proteins, which can cause deleterious effects. Mitochondria containing these deleterious STR mutations accumulate in cells and can produce deleterious proteins. Conclusions: We proposed that the accumulation of CNV of STRs in mitochondria may cause aging or diseases. Future tests of the CNV of STRs hypothesis help to ultimately reveal the genetic basis of mitochondrial DNA variation and its consequences (e.g., aging and diseases) in animals. Our study will lead to the reconsideration of the importance of STRs and a unified study of CNV of STRs with longer and shorter repeat units (particularly polynucleotides) in both nuclear and mt genomes.