Precise annotation of Drosophila mitochondrial genomes leads to insights into AT-rich regions

Liang, Guangcai; Mi, Dong; Jia, Chang; Yau, Tung On; Xu, Guofeng; Ruan, Jishou; Bu, Wenjun; Gao, Shan

doi:10.1016/j.mito.2022.06.006

Cited by 5 publications

(2 citation statements)

References 11 publications

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“…For further analysis, the 62-nt segments were divided into three regions ( Figure 5 ), I (−37,-13), II (−12, −1), and III (+1, 25) with AT-content of 65%, 80% and 65%, respectively. Region II of cp promoters in A. thaliana has the highest AT-content, which was consistent with a finding reported in our previous study of TISs in Drosophila mtDNAs [ 10 ]. Region II of mt promoters in Drosophila melanogaster has the AT-content of 100% ( Figure 5B ).…”

Section: Resultssupporting

confidence: 92%

PacBio full-length transcriptome analysis provides new insights into transcription of chloroplast genomes

Shi

Yan

et al. 2023

RNA Biology

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Chloroplast and mitochondrial DNA (cpDNA and mtDNA) are apart from nuclear DNA (nuDNA) in a eukaryotic cell. The transcription system of chloroplasts differs from those of mitochondria and eukaryotes. In contrast to nuDNA and animal mtDNA, the transcription of cpDNA is still not well understood, primarily due to the unresolved identification of transcription initiation sites (TISs) and transcription termination sites (TTSs) on the genome scale. In the present study, we characterized the transcription of chloroplast (cp) genes with greater accuracy and comprehensive information using PacBio full-length transcriptome data from Arabidopsis thaliana . The major findings included the discovery of four types of artifacts, the validation and correction of cp gene annotations, the exact identification of TISs that start with G, and the discovery of polyA-like sites as TTSs. Notably, we proposed a new model to explain cp transcription initiation and termination at the whole-genome level. Four types of artifacts, degraded RNAs and splicing intermediates deserve the attention from researchers working with PacBio full-length transcriptome data, as these contaminant sequences can lead to incorrect downstream analysis. Cp transcription initiates at multiple promoters and terminates at polyA-like sites. Our study provides new insights into cp transcription and new clues to study the evolution of promoters, TISs, TTSs and polyA tails of eukaryotic genes.

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Section: Resultssupporting

confidence: 92%

PacBio full-length transcriptome analysis provides new insights into transcription of chloroplast genomes

Shi

Yan

et al. 2023

RNA Biology

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“…The AT-contents of the three regions reached 65%, 80% and 65%, respectively. This nding was consistent with a nding reported in our previous study of TISs in Drosophila mtDNAs [10]. Transcription promoters of both A. thaliana cpDNA and Drosophila melanogaster mtDNA contain multiple short tandem repeats (STRs) and low complexity sequences that are composed of A and T (Figure 5B).…”

Section: Identi Cation Of Tiss With Further Analysissupporting

confidence: 92%

PacBio Full-length Transcriptome Analysis Provides New Insights into Transcription of Chloroplast Genomes

Gao

Shi

Yan

et al. 2022

Preprint

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Background: Chloroplast and mitochondrial DNA (cpDNA and mtDNA) are apart from nuclear DNA (nuDNA) in a eukaryotic cell. The transcription system of chloroplasts is different from those of mitochondria and eukaryotes. In contrast to mtDNA and nuDNA, the transcription of cpDNA remains unclear, mainly because the identification of the cp transcription initiation sites (TISs) and transcription termination sites (TTSs)remains unresolved. Results: In the present study, we characterized the transcription of cp genes with more comprehensive and accurate information using PacBio full-length transcriptome data of Arabidopsis thaliana. The main results included the discovery of four types of artifacts, the validation and correction of cp gene annotations, the discovery of polyA-like sites as TTSs and the exact identification of “GA”- and “GT”-type TISs on the genome scale. Notably, we proposed a new model to explain how the cptranscription initiates and terminates at the genome level. Conclusions: Four types of artifacts, degraded RNAs and splicing intermediates deserve the attention of every scientist who is working with PacBio full-length transcriptome data, as these contamination sequences could mislead the downstream analysis. The cp transcription initiates at multiple promoters and terminates at polyA-like sites. Our study provides new insights into the cp transcription and new clues to reveal the origins of promoters, TISs, TTSs and polyA tails of eukaryotic genes.

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PacBio full-length transcriptome analysis reveals the role of tRNA-like structures in RNA processing

Hu,

Yan,

Yan

et al. 2025

Cellular Signalling

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Precise annotation of Drosophila mitochondrial genomes leads to insights into AT-rich regions

Cited by 5 publications

References 11 publications

PacBio full-length transcriptome analysis provides new insights into transcription of chloroplast genomes

PacBio full-length transcriptome analysis provides new insights into transcription of chloroplast genomes

PacBio Full-length Transcriptome Analysis Provides New Insights into Transcription of Chloroplast Genomes

PacBio full-length transcriptome analysis reveals the role of tRNA-like structures in RNA processing

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