Browse
Submit Data
Databases
API
Help

Dataset Information

19 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The Full-Length Transcriptome Sequencing and Identification of Na⁺/H⁺ Antiporter Genes in Halophyte Nitraria tangutorum Bobrov.

ABSTRACT: Nitraria tangutorum Bobrov is a halophyte that is resistant to salt and alkali and is widely distributed in northwestern China. However, its genome has not been sequenced, thereby limiting studies on this particular species. For species without a reference genome, the full-length transcriptome is a convenient and rapid way to obtain reference gene information. To better study N. tangutorum, we used PacBio single-molecule real-time technology to perform full-length transcriptome analysis of this halophyte. In this study, a total of 21.83 Gb of data were obtained, and 198,300 transcripts, 51,875 SSRs (simple sequence repeats), 55,574 CDS (coding sequence), and 74,913 lncRNAs (long non-coding RNA) were identified. In addition, using this full-length transcriptome, we identified the key Na⁺/H⁺ antiporter (NHX) genes that maintain ion balance in plants and found that these are induced to express under salt stress. The results indicate that the full-length transcriptome of N. tangutorum can be used as a database and be utilized in elucidating the salt tolerance mechanism of N. tangutorum.

SUBMITTER: Zhu L

PROVIDER: S-EPMC8227117 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Full-Length Transcriptome Analysis of the Halophyte Nitraria sibirica Pall.

Project description:BackgroundNitraria sibirica Pall. is one of the pioneer tree species in saline-alkali areas due to its extreme salt tolerance. However, the lack of information on its genome limits the further exploration of the molecular mechanisms in N. sibirica under salt stress.MethodsIn this study, we used single-molecule real-time (SMRT) technology based on the PacBio Iso-Seq platform to obtain transcriptome data from N. sibirica under salt treatment for the first time, which is helpful for our in-depth analysis of the salt tolerance and molecular characteristics of N. sibirica.ResultsOur results suggested that a total of 234,508 circular consensus sequences (CCSs) with a mean read length of 2121 bp were obtained from the 19.26 Gb raw data. Furthermore, based on transcript cluster analysis, 93,713 consensus isoforms were obtained, including 92,116 high-quality isoforms. After removing redundant sequences, 49,240 non-redundant transcripts were obtained from high-quality isoforms. A total of 37,261 SSRs, 1816 LncRNAs and 47,314 CDSs, of which 40,160 carried complete ORFs, were obtained. Based on our transcriptome data, we also analyzed the coding genes of H+-PPase, and the results of both bioinformatics and functional analyses indicated that the gene prediction via full-length transcripts obtained by SMRT technology is reliable and effective. In summary, our research data obtained by SMRT technology provides more reliable and accurate information for the further analysis of the regulatory network and molecular mechanism of N. sibirica under salt stress.

| S-EPMC9032868 | biostudies-literature

Nitraria tangutorum

Project description:Nitraria tangutorum Transcriptome or Gene expression

| PRJNA273347 | ENA

Nitraria tangutorum

Project description:Nitraria tangutorum overview

| PRJNA728770 | ENA

Nitraria tangutorum

Project description:Nitraria tangutorum transcriptome raw data

| PRJNA675486 | ENA

Nitraria tangutorum

Project description:Nitraria tangutorum Raw sequence reads

| PRJNA728762 | ENA

NtCIPK9: A Calcineurin B-Like Protein-Interacting Protein Kinase From the Halophyte Nitraria tangutorum, Enhances Arabidopsis Salt Tolerance.

Project description:Calcineurin B-like protein-interacting protein kinases (CIPKs) play essential roles in plant abiotic stress response. In order to better understand salt tolerance, we cloned and analyzed the NtCIPK9 gene from the halophyte Nitraria tangutorum. Phylogenetic analysis shows that NtCIPK9 belongs to a sister clade with the Arabidopsis AtCIPK9 gene and is thought to localize to the plasma membrane. NtCIPK9 shows the highest expression level in the Nitraria tangutorum root under normal growth conditions, whereas after NaCl treatment, the highest expression was found in the blade. NtCIPK9-overexpressing Arabidopsis plants have a higher seed germination rate, longer root length, and displayed higher salt tolerance than wild type seedlings under salt stress conditions. Furthermore, NtCIPK9 overexpression might enhance the expression of genes related to K+ transportation after NaCl treatment. Thus, we conclude that NtCIPK9 increases transgenic plant salt tolerance and reduces damage associated with salt stress by promoting the expression of genes controlling ion homeostasis. Our results suggest that NtCIPK9 could serve as an ideal candidate gene to genetically engineer salt-tolerant plants.

| S-EPMC7472804 | biostudies-literature

Realizing the potential of full-length transcriptome sequencing.

Project description:Long-read sequencing holds great potential for transcriptome analysis because it offers researchers an affordable method to annotate the transcriptomes of non-model organisms. This, in turn, will greatly benefit future work on less-researched organisms like unicellular eukaryotes that cannot rely on large consortia to generate these transcriptome annotations. However, to realize this potential, several remaining molecular and computational challenges will have to be overcome. In this review, we have outlined the limitations of short-read sequencing technology and how long-read sequencing technology overcomes these limitations. We have also highlighted the unique challenges still present for long-read sequencing technology and provided some suggestions on how to overcome these challenges going forward. This article is part of a discussion meeting issue 'Single cell ecology'.

| S-EPMC6792442 | biostudies-literature

Water Addition Prolonged the Length of the Growing Season of the Desert Shrub Nitraria tangutorum in a Temperate Desert.

Project description:Climate models often predict that more extreme precipitation events will occur in arid and semiarid regions, where plant phenology is particularly sensitive to precipitation changes. To understand how increases in precipitation affect plant phenology, this study conducted a manipulative field experiment in a desert ecosystem of northwest China. In this study, a long-term in situ water addition experiment was conducted in a temperate desert in northwestern China. The following five treatments were used: natural rain plus an additional 0, 25, 50, 75, and 100% of the local mean annual precipitation. A series of phenological events, including leaf unfolding (onset, 30%, 50%, and end of leaf unfolding), cessation of new branch elongation (30, 50, and 90%), and leaf coloration (80% of leaves turned yellow), of the locally dominant shrub Nitraria tangutorum were observed from 2012 to 2018. The results showed that on average, over the seven-year-study and in all treatments water addition treatments advanced the spring phenology (30% of leaf unfolding) by 1.29-3.00 days, but delayed the autumn phenology (80% of leaves turned yellow) by 1.18-11.82 days. Therefore, the length of the growing season was prolonged by 2.11-13.68 days, and autumn phenology contributed more than spring phenology. In addition, water addition treatments delayed the cessation of new branch elongation (90%) by 5.82-12.61 days, and nonlinear relationships were found between the leaves yellowing (80% of leaves) and the amount of watering. Linear relationships were found between the cessation of new branch elongation (90%), the length of the growing season, and amount of water addition. The two response patterns to water increase indicated that predictions of phenological events in the future should not be based on one trend only.

| S-EPMC7386313 | biostudies-literature

SMRT sequencing of full-length transcriptome of seagrasses Zostera japonica.

Project description:Seagrass meadows are among the four most productive marine ecosystems in the world. Zostera japonica (Z. japonica) is the most widely distributed species of seagrass in China. However, there is no reference genome or transcriptome available for Z. japonica, impeding progress in functional genomic and molecular ecology studies in this species. Temperature is the main factor that controls the distribution and growth of seagrass around the world, yet how seagrass responds to heat stress remains poorly understood due to the lack of genomic and transcriptomic data. In this study, we applied a combination of second- and third-generation sequencing technologies to sequence full-length transcriptomes of Z. japonica. In total, we obtained 58,134 uniform transcripts, which included 46,070 high-quality full-length transcript sequences. We identified 15,411 simple sequence repeats, 258 long non-coding RNAs and 28,038 open reading frames. Exposure to heat elicited a complex transcriptional response in genes involved in posttranslational modification, protein turnover and chaperones. Overall, our study provides the first large-scale full-length trascriptome in Zostera japonica, allowing for structural, functional and comparative genomics studies in this important seagrass species. Although previous studies have focused specifically on heat shock proteins, we found that examination of other heat stress related genes is important for studying response to heat stress in seagrass. This study provides a genetic resource for the discovery of genes related to heat stress tolerance in this species. Our transcriptome can be further utilized in future studies to understand the molecular adaptation to heat stress in Zostera japonica.

| S-EPMC6787188 | biostudies-literature

SMRT sequencing of the full-length transcriptome of Gekko gecko.

Project description:Tokay Gecko (Gekko gecko) is a rare and endangered medicinal animal in China. Its dry body has been used as an anti-asthmatic agent for two thousand years. To date, the genome and transcriptome of this species remain poorly understood. Here, we adopted single molecule real-time (SMRT) sequencing to obtain full-length transcriptome data and characterized the transcriptome structure. We identified 882,273 circular consensus (CCS) reads, including 746,317 full-length nonchimeric (FLNC) reads. The transcript cluster analysis revealed 212,964 consensus sequences, including 203,994 high-quality isoforms. In total, 111,372 of 117,888 transcripts were successfully annotated against eight databases (Nr, eggNOG, Swiss-Prot, GO, COG, KOG, Pfam and KEGG). Furthermore, 23,877 alternative splicing events, 169,128 simple sequence repeats (SSRs), 10,437 lncRNAs and 7,932 transcription factors were predicted across all transcripts. To our knowledge, this report is the first to document the G. gecko transcriptome using SMRT sequencing. The full-length transcript data might accelerate transcriptome research and lay the foundation for further research on G. gecko.

| S-EPMC8880673 | biostudies-literature