Long-read RNA sequencing can probe organelle genome pervasive transcription

Author:

Sanita Lima Matheus12ORCID,Silva Domingues Douglas34ORCID,Rossi Paschoal Alexandre56ORCID,Smith David Roy12ORCID

Affiliation:

1. Department of Biology , , 1151 Richmond Street, London, Ontario N6A 5B7 , Canada

2. Western University , , 1151 Richmond Street, London, Ontario N6A 5B7 , Canada

3. Department of Genetics , “Luiz de Queiroz” College of Agriculture, , Avenida Padua Dias 11, Piracicaba, SP 13418-900 , Brazil

4. University of São Paulo , “Luiz de Queiroz” College of Agriculture, , Avenida Padua Dias 11, Piracicaba, SP 13418-900 , Brazil

5. Department of Computer Science , Bioinformatics and Pattern Recognition Group (BIOINFO-CP), , Avenida Alberto Carazzai 1640, Cornélio Procópio, PR 86300000 , Brazil

6. Federal University of Technology – Paraná – UTFPR , Bioinformatics and Pattern Recognition Group (BIOINFO-CP), , Avenida Alberto Carazzai 1640, Cornélio Procópio, PR 86300000 , Brazil

Abstract

Abstract 40 years ago, organelle genomes were assumed to be streamlined and, perhaps, unexciting remnants of their prokaryotic past. However, the field of organelle genomics has exposed an unparallel diversity in genome architecture (i.e. genome size, structure, and content). The transcription of these eccentric genomes can be just as elaborate – organelle genomes are pervasively transcribed into a plethora of RNA types. However, while organelle protein-coding genes are known to produce polycistronic transcripts that undergo heavy posttranscriptional processing, the nature of organelle noncoding transcriptomes is still poorly resolved. Here, we review how wet-lab experiments and second-generation sequencing data (i.e. short reads) have been useful to determine certain types of organelle RNAs, particularly noncoding RNAs. We then explain how third-generation (long-read) RNA-Seq data represent the new frontier in organelle transcriptomics. We show that public repositories (e.g. NCBI SRA) already contain enough data for inter-phyla comparative studies and argue that organelle biologists can benefit from such data. We discuss the prospects of using publicly available sequencing data for organelle-focused studies and examine the challenges of such an approach. We highlight that the lack of a comprehensive database dedicated to organelle genomics/transcriptomics is a major impediment to the development of a field with implications in basic and applied science.

Funder

Natural Sciences and Engineering Research Council of Canada

Fundação Araucária

Publisher

Oxford University Press (OUP)

Cited by 1 articles. 订阅此论文施引文献 订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3