Abstract:
:Nanopore sequencing from Oxford Nanopore Technologies (ONT) and Pacific BioSciences (PacBio) single-molecule real-time (SMRT) long-read isoform sequencing (Iso-Seq) are revolutionizing the way transcriptomes are analyzed. These methods offer many advantages over most widely used high-throughput short-read RNA sequencing (RNA-Seq) approaches and allow a comprehensive analysis of transcriptomes in identifying full-length splice isoforms and several other post-transcriptional events. In addition, direct RNA-Seq provides valuable information about RNA modifications, which are lost during the PCR amplification step in other methods. Here, we present a comprehensive summary of important applications of these technologies in plants, including identification of complex alternative splicing (AS), full-length splice variants, fusion transcripts, and alternative polyadenylation (APA) events. Furthermore, we discuss the impact of the newly developed nanopore direct RNA-Seq in advancing epitranscriptome research in plants. Additionally, we summarize computational tools for identifying and quantifying full-length isoforms and other co/post-transcriptional events and discussed some of the limitations with these methods. Sequencing of transcriptomes using these new single-molecule long-read methods will unravel many aspects of transcriptome complexity in unprecedented ways as compared to previous short-read sequencing approaches. Analysis of plant transcriptomes with these new powerful methods that require minimum sample processing is likely to become the norm and is expected to uncover novel co/post-transcriptional gene regulatory mechanisms that control biological outcomes during plant development and in response to various stresses.
journal_name
Front Genetjournal_title
Frontiers in geneticsauthors
Zhao L,Zhang H,Kohnen MV,Prasad KVSK,Gu L,Reddy ASNdoi
10.3389/fgene.2019.00253subject
Has Abstractpub_date
2019-03-21 00:00:00pages
253issn
1664-8021journal_volume
10pub_type
杂志文章,评审abstract::Homozygous and compound heterozygous mutations in GNB5 gene have been associated with a wide spectrum of clinical presentations, ranging from neurodevelopmental issues with or without cardiac arrhythmia (LADCI) to severe developmental delay with epileptic encephalopathy, retinal dystrophy, and heart rhythm abnormaliti...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00399
更新日期:2020-05-13 00:00:00
abstract::Colorectal cancer (CRC) is the third most commonly diagnosed type of cancer worldwide. The mechanisms leading to the progression of CRC are involved in both genetic and epigenetic regulations. In this study, we applied systems biology methods to identify potential biomarkers and conduct drug discovery in a computation...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00117
更新日期:2020-03-06 00:00:00
abstract::Analysis of the relationships among wild species of section Moutan in the plant genus Paeonia has traditionally been problematic. Interspecies relationships cannot be effectively determined using phenotypic traits alone or through analysis of nuclear or chloroplast DNA fragments. Elucidation of complete chloroplast ge...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00980
更新日期:2020-09-18 00:00:00
abstract::People want to live long, healthy lives. Previous surveys suggest very limited interest in much longer lifespans, but we show that stipulating good health changes responses to favor longer lives by an order of magnitude. Advances in aging research hold out hope for greatly slowed aging with associated good health. Und...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2015.00353
更新日期:2016-01-20 00:00:00
abstract::The Apelin (APLN)/apelin receptor (APLNR) signaling pathway is a newly identified regulator in various cardiovascular diseases, which is considered as a candidate pathway for the occurrence of coronary heart disease (CHD), depression, and anxiety. The goal of this study was to investigate the association between APLN/...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00893
更新日期:2020-08-11 00:00:00
abstract::RNA is a unique bio-macromolecule that can both record genetic information and perform biological functions in a variety of molecular processes, including transcription, splicing, translation, and even regulating protein function. RNAs adopt specific three-dimensional conformations to enable their functions. Experimen...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2020.574485
更新日期:2020-10-26 00:00:00
abstract::Genomic breed composition (GBC) of an individual animal refers to the partition of its genome according to the inheritance from its ancestors or ancestral breeds. For crossbred or composite animals, knowing their GBC is useful to estimate heterosis, to characterize their actual inheritance from foundation breeds, and ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.546052
更新日期:2020-10-30 00:00:00
abstract::Background: The aim of this study was to explore the Human Papillomavirus (HPV) genotype composition and intra-genotype variants within individual samples of low- and high-grade cervical cytology by deep sequencing. Clinical, cytological, sequencing, and functional/structural data were forged into an integrated varian...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00489
更新日期:2019-05-24 00:00:00
abstract::In the last decades, genome-wide association studies (GWAS) have uncovered tens of thousands of associations between common genetic variants and complex diseases. However, these statistical associations can rarely be interpreted functionally and mechanistically. As the majority of the disease-associated variants are l...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00714
更新日期:2019-08-16 00:00:00
abstract::Familial hemophagocytic lymphohistiocytosis Type 2 (FHL2) associated central nervous system (CNS) involvement is less understood in children, especially when considering neurologic manifestations as part of the initial presentation. We conducted a retrospective review of the clinical manifestations and genetic abnorma...
journal_title:Frontiers in genetics
pub_type:
doi:10.3389/fgene.2020.00126
更新日期:2020-03-04 00:00:00
abstract::Studies in rats and mice have established that maternal nutrition induces epigenetic modifications, sometimes permanently, that alter gene expression in the fetus, which in turn leads to phenotypic changes. However, limited data is available on the influence of maternal diet on epigenetic modifications and gene expres...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2013.00049
更新日期:2013-04-05 00:00:00
abstract::Trauma is a leading cause of morbidity and mortality. It is unclear why some trauma victims follow a complicated clinical course and die, while others, with apparently similar injury characteristics, do not. Interpatient genomic differences, in the form of single nucleotide polymorphisms (SNPs), have been associated p...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.01115
更新日期:2019-11-08 00:00:00
abstract::The multi-subunit protein complex, cohesin, is responsible for sister chromatid cohesion during cell division. The interaction of cohesin with DNA is controlled by a number of additional regulatory proteins. Mutations in cohesin, or its regulators, cause a spectrum of human developmental syndromes known as the "cohesi...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2012.00171
更新日期:2012-09-12 00:00:00
abstract::Domestication to captive rearing conditions, along with targeted selective breeding have genetic consequences that vary from those in wild environments. Nile tilapia (Oreochromis niloticus) is one of the most translocated and farmed aquaculture species globally, farmed throughout Asia, North and South America, and its...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.567969
更新日期:2020-10-15 00:00:00
abstract::Production animals are constantly subjected to early adverse environmental conditions that influence the adult phenotype and produce epigenetic effects. CpG dinucleotide methylation in red blood cells (RBC) could be a useful epigenetic biomarker to identify animals subjected to chronic stress in the production environ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.508809
更新日期:2020-11-02 00:00:00
abstract::Normalization of cDNA is widely used to improve the coverage of rare transcripts in analysis of transcriptomes employing next-generation sequencing. Recently, long-read technology has been emerging as a powerful tool for sequencing and construction of transcriptomes, especially for complex genomes containing highly si...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00654
更新日期:2019-07-23 00:00:00
abstract::Excessive fat deposition can cause chicken health problem, and affect production efficiency by causing great economic losses to the industry. However, the molecular underpinnings of the complex adiposity trait remain elusive. In the current study, we constructed and compared the gene co-expression networks on four tra...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00537
更新日期:2020-05-29 00:00:00
abstract::In genome wide association studies (GWAS), family-based studies tend to have less power to detect genetic associations than population-based studies, such as case-control studies. This can be an issue when testing if genes in a family-based GWAS have a direct effect on the phenotype of interest over and above their po...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2013.00243
更新日期:2013-11-21 00:00:00
abstract::Objective: Adrenocortical carcinoma (ACC) is a rare but aggressive malignant cancer that has been attracting growing attention over recent decades. This study aims to integrate protein interaction networks with gene expression profiles to identify potential biomarkers with prognostic value in silico. Methods: Three mi...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00821
更新日期:2019-09-11 00:00:00
abstract::Autosomal dwarfism (adw) in chickens is a growth deficiency caused by a recessive mutation. Characteristic for adw is an approximately 30% growth reduction with short shank. The adw variant was first recognized in the Cornell K-strain of White Leghorns, but the genetic causal variant remained unknown. To identify the ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00193
更新日期:2018-06-07 00:00:00
abstract::Exosomes are biomolecular nanostructures released from cells. They carry specific biomolecular information and are mainly researched for their exquisite properties as a biomarker source and delivery system. We introduce exosomes in the context of other extracellular vesicles, describe their biophysical isolation and c...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2018.00092
更新日期:2018-03-27 00:00:00
abstract::The Galway sheep population is the only native Irish sheep breed and this livestock genetic resource is currently categorised as 'at-risk'. In the present study, comparative population genomics analyses of Galway sheep and other sheep populations of European origin were used to investigate the microevolution and recen...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00927
更新日期:2019-10-08 00:00:00
abstract::In recent years, there has been an explosive increase in the amount of bioinformatics data produced, but data are not information. The purpose of bioinformatics research is to obtain information with biological significance from large amounts of data. Multiple sequence alignment is widely used in sequence homology det...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00105
更新日期:2020-02-27 00:00:00
abstract::Human exposure to mercury is a serious problem of public health in Amazon. As in other vulnerable populations throughout the world, Amazonian riverine populations are chronically exposed to this metal and some symptoms of mercury intoxication were already detected in these populations. However, studies on the genetic ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00285
更新日期:2018-07-27 00:00:00
abstract::Leukocyte telomere length is believed to measure cellular aging in humans, and short leukocyte telomere length is associated with increased risks of late onset diseases, including cardiovascular disease, dementia, etc. Many studies have shown that leukocyte telomere length is a heritable trait, and several candidate g...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2013.00310
更新日期:2014-01-17 00:00:00
abstract::Alport syndrome (AS) is a rare and inherited renal disorder with an autosomal recessive mode of inheritance. AS patients usually manifest with hematuria and progressive renal disorder also occasionally accompanied by hearing loss and ophthalmic disease. Germline variants in collagen type IV α-4 (COL4A4) gene lead to a...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00748
更新日期:2019-01-28 00:00:00
abstract::Pacu (Piaractus mesopotamicus) is a Neotropical fish of major importance for South American aquaculture. Septicemia caused by Aeromonas hydrophila bacteria is currently considered a substantial threat for pacu aquaculture that have provoked infectious disease outbreaks with high economic losses. The understanding of m...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00604
更新日期:2020-06-09 00:00:00
abstract::STI/HOP functions as a co-chaperone of HSP90 and HSP70 whose molecular function has largely been being restricted as an adaptor protein. However, its role in thermotolerance is not well explored. In this article, we have identified six members of the TaSTI family, which were named according to their distribution on gr...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00873
更新日期:2020-08-19 00:00:00
abstract::Cell viability and gene expression profiles are altered in cellular models of neurodegenerative disorders such as Huntington's Disease (HD). Using the yeast model system, we show that the SUMO-targeted ubiquitin ligase (STUbL) Slx5 reduces the toxicity and abnormal transcriptional activity associated with a mutant, ag...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00379
更新日期:2018-09-18 00:00:00
abstract::Few studies have been conducted to explore the influence of the catechol-o-methyltransferase (COMT) genotype on the severity of and treatment efficacy on auditory verbal hallucination (AVH) symptoms in healthy individuals with AVHs (Hi-AVHs). We hypothesized that the efficacy of dopamine antagonist treatment on AVHs i...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00092
更新日期:2019-03-06 00:00:00