Transcriptome analysis reveals long noncoding RNAs involved in fiber development in cotton (Gossypium arboreum)

Zou, Changsong; Wang, Qiaolian; Lu, Changming; Wei, Yang; Zhang, Youping; Cheng, Hongyan; Xu, Feng; Prosper, Mtawa Andrew; Song, Guoli

doi:10.1007/s11427-016-5000-2

Cited by 80 publications

(51 citation statements)

References 50 publications

(72 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…are abundant bulbous flowers worldwide, but their genome and miRNAs have not yet been explored. Information on key genes and miRNAs can be obtained through deep sequencing (Candar-Cakir et al, 2016; Cheng et al, 2016; Zhang W. et al, 2016; Zou et al, 2016). Thus, using this method, we pioneered research on the identification of miRNAs during SE in Lilium .…”

Section: Discussionmentioning

confidence: 99%

Small RNA and Transcriptome Sequencing Reveal a Potential miRNA-Mediated Interaction Network That Functions during Somatic Embryogenesis in Lilium pumilum DC. Fisch.

et al. 2017

View full text Add to dashboard Cite

Plant somatic embryos are widely used in the fields of germplasm conservation, breeding for genetic engineering and artificial seed production. MicroRNAs (miRNAs) play pivotal roles in somatic embryogenesis (SE) regulation. However, their regulatory roles during various stages of SE remain unclear. In this study, six types of embryogenic samples of Lilium pumilum DC. Fisch., including organogenic callus, embryogenic callus induced for 4 weeks, embryogenic callus induced for 6 weeks, globular embryos, torpedo embryos and cotyledon embryos, were prepared for small RNA sequencing. The results revealed a total of 2,378,760 small RNA reads, among which the most common size was 24 nt. Four hundred and fifty-two known miRNAs, belonging to more than 86 families, 57 novel miRNAs and 40 miRNA*s were identified. The 86 known miRNA families were sorted according to an alignment with their homologs across 24 land plants into the following four categories: 23 highly conserved, 4 moderately conserved, 15 less conserved and 44 species-specific miRNAs. Differentially expressed known miRNAs were identified during various stages of SE. Subsequently, the expression levels of 12 differentially expressed miRNAs and 4 targets were validated using qRT-PCR. In addition, six samples were mixed in equal amounts for transcript sequencing, and the sequencing data were used as transcripts for miRNA target prediction. A total of 66,422 unigenes with an average length of 800 bp were assembled from 56,258,974 raw reads. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment indicated that 38,004 and 15,497 unigenes were successfully assigned to GO terms and KEGG pathways, respectively. Among the unigenes, 2,182 transcripts were predicted to be targets for 396 known miRNAs. The potential targets of the identified miRNAs were mostly classified into the following GO terms: cell, binding and metabolic process. Enriched KEGG analysis demonstrated that carbohydrate metabolism was the predominant pathway in Lilium SE. Thus, we performed systemic characterization, homology comparisons and profiling of miRNA expression, and we constructed an miRNA-target network during Lilium SE for the first time. Our findings establish a foundation for the further exploration of critical genes and elucidation of SE in Lilium.

show abstract

Section: Discussionmentioning

confidence: 99%

Small RNA and Transcriptome Sequencing Reveal a Potential miRNA-Mediated Interaction Network That Functions during Somatic Embryogenesis in Lilium pumilum DC. Fisch.

et al. 2017

View full text Add to dashboard Cite

show abstract

“…Generally, long non‐coding RNAs (lncRNAs) are transcripts of more than 200 nucleotides (nt) in length that possess no apparent coding sequence (CDS) or open reading frame (Fan et al ., ; Wang et al ., ). A number of lncRNAs have recently been identified in plant species due to rapid progress in omics sequencing technology (Li et al ., ; Zou et al ., ), including Arabidopsis (Ben Amor et al ., ; Liu et al ., ; Di et al ., ; Wang et al ., ), rice (Zhang et al ., ), maize (Li et al ., ; Fan et al ., ), wheat (Xin et al ., ), cotton (Wang et al ., ; Zou et al ., ), tomato (Wang et al ., , ; Zhu et al ., ), cucumber (Hao et al ., ), Chinese cabbage (Song et al ., ), Populus (Shuai et al ., ; Chen et al ., ) and others. In particular, studies on plant lncRNAs are far behind those in humans and animals (Liu et al ., ).…”

Section: Introductionmentioning

confidence: 99%

Comparative transcriptome analysis between resistant and susceptible tomato allows the identification of lncRNA16397 conferring resistance to Phytophthora infestans by co‐expressing glutaredoxin

et al. 2017

View full text Add to dashboard Cite

The rapid development of omics sequencing technology has facilitated the identification of thousands of long non-coding (lnc)RNAs in plant species, but the role of lncRNAs in plant-pathogen interactions remains largely unexplored. We used comparative transcriptome analysis of Phytophthora infestans-resistant and -susceptible tomatoes to identify differentially expressed genes (DEGs) and lncRNAs (DELs), and examine lncRNA-mRNA networks. A total of 1037 DEGs and 688 DELs were identified between P. infestans-resistant and -susceptible tomatoes. The co-localization networks, including 128 DEGs and 127 DELs, were performed. We found that lncRNA16397 acted as an antisense transcript of SlGRX22 to regulate its expression, and also induced SlGRX21 expression when lncRNA16397 was overexpressed. In addition, disease symptoms and reactive oxygen species (ROS) accumulation in tomatoes overexpressing lncRNA16397 and SpGRX were fewer and lower than those in wild-type after P. infestans infection. This result suggests that tomato lncRNA16397 induces SlGRX expression to reduce ROS accumulation and alleviate cell membrane injury, resulting in enhanced resistance to P. infestans. Our results provide insight into lncRNAs involved in the response of tomato to P. infestans infection, demonstrate that the lncRNA16397-GRXs network is an important component of the P. infestans network in tomato, and provide candidates for breeding to enhance biotic stress-resistance in tomato.

show abstract

“…(Yu et al ., ), populus (Shuai et al ., ), Triticum aestivum (wheat; Xin et al ., ), Gossypium spp . (cotton; Wang et al ., ) Gossypium arboreum (cotton; Zou et al ., ), Solanum lycopersicum (tomato; Wang et al ., ; Zhu et al ., ; Wang et al ., ), Cucumis sativus (cucumber; Hao et al ., ) and other plants. Most of these genome‐wide studies have focused on identifying novel lncRNAs and profiling expression patterns, but some of them have assessed transcription factor regulation at the transcriptional level (Di et al ., ).…”

Section: Introductionmentioning

confidence: 99%

Stress‐responsive regulation of long non‐coding RNA polyadenylation in Oryza sativa

Yuan

Yang

et al. 2018

The Plant Journal

View full text Add to dashboard Cite

Recently, long non-coding RNAs (lncRNAs) have been demonstrated to be involved in many biological processes of plants; however, a systematic study on transcriptional and, in particular, post-transcriptional regulation of stress-responsive lncRNAs in Oryza sativa (rice) is lacking. We sequenced three types of RNA libraries (poly(A)+, poly(A)- and nuclear RNAs) under four abiotic stresses (cold, heat, drought and salt). Based on an integrative bioinformatics approach and ~200 high-throughput data sets, ~170 of which have been published, we revealed over 7000 lncRNAs, nearly half of which were identified for the first time. Notably, we found that the majority of the ~500 poly(A) lncRNAs that were differentially expressed under stress were significantly downregulated, but approximately 25% were found to have upregulated non-poly(A) forms. Moreover, hundreds of lncRNAs with downregulated polyadenylation (DPA) tend to be highly conserved, show significant nuclear retention and are co-expressed with protein-coding genes that function under stress. Remarkably, these DPA lncRNAs are significantly enriched in quantitative trait loci (QTLs) for stress tolerance or development, suggesting their potential important roles in rice growth under various stresses. In particular, we observed substantially accumulated DPA lncRNAs in plants exposed to drought and salt, which is consistent with the severe reduction of RNA 3'-end processing factors under these conditions. Taken together, the results of this study reveal that polyadenylation and subcellular localization of many rice lncRNAs are likely to be regulated at the post-transcriptional level. Our findings strongly suggest that many upregulated/downregulated lncRNAs previously identified by traditional RNA-seq analyses need to be carefully reviewed to assess the influence of post-transcriptional modification.

show abstract

Transcriptome analysis reveals long noncoding RNAs involved in fiber development in cotton (Gossypium arboreum)

Cited by 80 publications

References 50 publications

Small RNA and Transcriptome Sequencing Reveal a Potential miRNA-Mediated Interaction Network That Functions during Somatic Embryogenesis in Lilium pumilum DC. Fisch.

Small RNA and Transcriptome Sequencing Reveal a Potential miRNA-Mediated Interaction Network That Functions during Somatic Embryogenesis in Lilium pumilum DC. Fisch.

Comparative transcriptome analysis between resistant and susceptible tomato allows the identification of lncRNA16397 conferring resistance to Phytophthora infestans by co‐expressing glutaredoxin

Stress‐responsive regulation of long non‐coding RNA polyadenylation in Oryza sativa

Contact Info

Product

Resources

About