scholarly journals Characterization of full-length transcriptome in Saccharum officinarum and molecular insights into tiller development

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Haifeng Yan ◽  
Huiwen Zhou ◽  
Hanmin Luo ◽  
Yegeng Fan ◽  
Zhongfeng Zhou ◽  
...  
Keyword(s):  
Carbon Fixation ◽  
Developmental Stages ◽  
Genomic Data ◽  
Saccharum Officinarum ◽  
Full Length ◽  
Rna Seq ◽  
Pyruvate Phosphate Dikinase ◽  
Sugarcane Yield ◽  
Tiller Bud

Abstract Background Although extensive breeding efforts are ongoing in sugarcane (Saccharum officinarum L.), the average yield is far below the theoretical potential. Tillering is an important component of sugarcane yield, however, the molecular mechanism underlying tiller development is still elusive. The limited genomic data in sugarcane, particularly due to its complex and large genome, has hindered in-depth molecular studies. Results Herein, we generated full-length (FL) transcriptome from developing leaf and tiller bud samples based on PacBio Iso-Seq. In addition, we performed RNA-seq from tiller bud samples at three developmental stages (T0, T1 and T2) to uncover key genes and biological pathways involved in sugarcane tiller development. In total, 30,360 and 20,088 high-quality non-redundant isoforms were identified in leaf and tiller bud samples, respectively, representing 41,109 unique isoforms in sugarcane. Likewise, we identified 1063 and 1037 alternative splicing events identified in leaf and tiller bud samples, respectively. We predicted the presence of coding sequence for 40,343 isoforms, 98% of which was successfully annotated. Comparison with previous FL transcriptomes in sugarcane revealed 2963 unreported isoforms. In addition, we characterized 14,946 SSRs from 11,700 transcripts and 310 lncRNAs. By integrating RNA-seq with the FL transcriptome, 468 and 57 differentially expressed genes (DEG) were identified in T1vsT0 and T2vsT0, respectively. Strong up-regulation of several pyruvate phosphate dikinase and phosphoenolpyruvate carboxylase genes suggests enhanced carbon fixation and protein synthesis to facilitate tiller growth. Similarly, up-regulation of linoleate 9S-lipoxygenase and lipoxygenase genes in the linoleic acid metabolism pathway suggests high synthesis of key oxylipins involved in tiller growth and development. Conclusions Collectively, we have enriched the genomic data available in sugarcane and provided candidate genes for manipulating tiller formation and development, towards productivity enhancement in sugarcane.

scholarly journals Single-Molecule Long-Read Sequencing Reveals the Diversity of Full-Length Transcripts in Leaves of Gnetum (Gnetales)

2019 ◽  
Vol 20 (24) ◽  
pp. 6350 ◽  
Author(s):  
Nan Deng ◽  
Chen Hou ◽  
Fengfeng Ma ◽  
Caixia Liu ◽  
Yuxin Tian
Keyword(s):  
Single Molecule ◽  
Developmental Stages ◽  
Alternative Polyadenylation ◽  
Full Length ◽  
Stomatal Development ◽  
Rna Seq ◽  
Leaf Transcriptome ◽  
Long Read ◽  
Non Coding Rnas ◽  
A Site

The limitations of RNA sequencing make it difficult to accurately predict alternative splicing (AS) and alternative polyadenylation (APA) events and long non-coding RNAs (lncRNAs), all of which reveal transcriptomic diversity and the complexity of gene regulation. Gnetum, a genus with ambiguous phylogenetic placement in seed plants, has a distinct stomatal structure and photosynthetic characteristics. In this study, a full-length transcriptome of Gnetum luofuense leaves at different developmental stages was sequenced with the latest PacBio Sequel platform. After correction by short reads generated by Illumina RNA-Seq, 80,496 full-length transcripts were obtained, of which 5269 reads were identified as isoforms of novel genes. Additionally, 1660 lncRNAs and 12,998 AS events were detected. In total, 5647 genes in the G. luofuense leaves had APA featured by at least one poly(A) site. Moreover, 67 and 30 genes from the bHLH gene family, which play an important role in stomatal development and photosynthesis, were identified from the G. luofuense genome and leaf transcripts, respectively. This leaf transcriptome supplements the reference genome of G. luofuense, and the AS events and lncRNAs detected provide valuable resources for future studies of investigating low photosynthetic capacity of Gnetum.

scholarly journals SMRT sequencing of the full-length transcriptome of the Rhynchophorus ferrugineus (Coleoptera: Curculionidae)

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9133 ◽  
Author(s):  
Hongjun Yang ◽  
Danping Xu ◽  
Zhihang Zhuo ◽  
Jiameng Hu ◽  
Baoqian Lu
Keyword(s):  
Developmental Stages ◽  
Average Length ◽  
Instar Larva ◽  
Full Length ◽  
Molecular Characteristics ◽  
Rhynchophorus Ferrugineus ◽  
Rna Seq ◽  
Male Adult ◽  
Palm Trees ◽  
Development Analysis

Background Red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae) is one of the most destructive insects for palm trees in the world. However, its genome resources are still in the blank stage, which limits the study of molecular and growth development analysis. Methods In this study, we used PacBio Iso-Seq and Illumina RNA-seq to first generate transcriptome from three developmental stages of R. ferrugineus (pupa, 7th larva, female and male) to increase our understanding of the life cycle and molecular characteristics of R. ferrugineus. Results A total of 63,801 nonredundant full-length transcripts were generated with an average length of 2,964 bp from three developmental stages, including the 7th instar larva, pupa, female adult and male adult. These transcripts showed a high annotation rate in seven public databases, with 54,999 (86.20%) successfully annotated. Meanwhile, 2,184 alternative splicing (AS) events, 2,084 transcription factors (TFs), 66,230 simple sequence repeats (SSR) and 9,618 Long noncoding RNAs (lncRNAs) were identified. In summary, our results provide a new source of full-length transcriptional data and information for the further study of gene expression and genetics in R. ferrugineus.

scholarly journals Transcriptome profiling for floral development in reblooming cultivar ‘High Noon’ of Paeonia suffruticosa

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Yanting Chang ◽  
Tao Hu ◽  
Wenbo Zhang ◽  
Lin Zhou ◽  
Yan Wang ◽  
...  
Keyword(s):  
Flower Development ◽  
Floral Development ◽  
Developmental Stages ◽  
Transcriptome Profiling ◽  
Full Length ◽  
Rna Seq ◽  
Paeonia Suffruticosa ◽  
Tree Peony ◽  
Flower Bud ◽  
High Noon

Abstract Tree peony (Paeonia suffruticosa Andrew) is a popular ornamental plant due to its large, fragrant and colorful flowers. The floral development is the most important event in its lifecycle. To explore the mechanism that regulate flower development, we sequenced the flower bud transcriptomes of ‘High Noon’, a reblooming cultivar of P. suffruticosa × P. lutea, using both full-length isoform-sequencing (ISO-seq) and RNA-seq were sequenced. A total of 15.94 Gb raw data were generated in full-length transcriptome sequencing of the 3 floral developmental stages, resulting 0.11 M protein-coding transcripts. Over 457.0 million reads were obtained by RNA-seq in the 3 floral buds. Here, we openly released the full-length transcriptome database of ‘High Noon’ and RNA-seq database of floral development. These databases can provide a fundamental genetic information of tree peony to investigate its transcript structure, variants and evolution. Data will facilitate to deep analyses of the transcriptome for flower development.

scholarly journals Identification and characterization of circular RNAs in Ganoderma lucidum

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Junjie Shao ◽  
Liqiang Wang ◽  
Xinyue Liu ◽  
Meng Yang ◽  
Haimei Chen ◽  
...  
Keyword(s):  
Ganoderma Lucidum ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Circular Rnas ◽  
Rna Seq ◽  
Polysaccharide Biosynthesis ◽  
Genome Wide ◽  
A Genome ◽  
Positive Correlations

Abstract Circular RNAs (circRNAs) play important roles in animals, plants, and fungi. However, no circRNAs have been reported in Ganoderma lucidum. Here, we carried out a genome-wide identification of the circRNAs in G.lucidum using RNA-Seq data, and analyzed their features. In total, 250 and 2193 circRNAs were identified from strand-specific RNA-seq data generated from the polyA(−) and polyA(−)/RNase R-treated libraries, respectively. Six of 131 (4.58%) predicted circRNAs were experimentally confirmed. Across three developmental stages, 731 exonic circRNAs (back spliced read counts ≥ 5) and their parent genes were further analyzed. CircRNAs were preferred originating from exons with flanking introns, and the lengths of the flanking intron were longer than those of the control introns. A total of 200 circRNAs were differentially expressed across the three developmental stages of G. lucidum. The expression profiles of 119 (16.3%) exonic circRNAs and their parent genes showed significant positive correlations (r ≥ 0.9, q < 0.01), whereas 226 (30.9%) exonic circRNAs and their parent genes exhibited significant negative correlations (r ≤ −0.9, q < 0.01), in which 53 parent genes are potentially involved in the transcriptional regulation, polysaccharide biosynthesis etc. Our results indicated that circRNAs are present in G. lucidum, with potentially important regulatory roles.

scholarly journals Integration of a Computational Pipeline for Dynamic Inference of Gene Regulatory Networks in Single Cells

2019 ◽  
Author(s):  
Kyung Dae Ko ◽  
Stefania Dell’Orso ◽  
Aster H. Juan ◽  
Vittorio Sartorelli
Keyword(s):  
Prior Knowledge ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Developmental Stages ◽  
Individual Cell ◽  
Single Cells ◽  
Rna Seq ◽  
Gene Regulatory ◽  
Molecular Expression

SUMMARYSingle-cell RNA-seq permits the characterization of the molecular expression states of individual cells. Several methods have been developed to spatially and temporally resolve individual cell populations. However, these methods are not always integrated and some of them are constrained by prior knowledge. Here, we present an integrated pipeline for inference of gene regulatory networks. The pipeline does not rely on prior knowledge, it improves inference accuracy by integrating signatures from different data dimensions and facilitates tracing variation of gene expression by visualizing gene-interacting patterns of co-expressed gene regulatory networks at distinct developmental stages.

scholarly journals Comparative Transcriptome Analysis Combining SMRT- and Illumina-Based RNA-Seq Identifies Potential Candidate Genes Involved in Betalain Biosynthesis in Pitaya Fruit

2020 ◽  
Vol 21 (9) ◽  
pp. 3288
Author(s):  
Yawei Wu ◽  
Juan Xu ◽  
Xiumei Han ◽  
Guang Qiao ◽  
Kun Yang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Single Molecule ◽  
Developmental Stages ◽  
Full Length ◽  
Reference Database ◽  
White Pulp ◽  
Potential Candidate ◽  
Rna Seq ◽  
Smrt Sequencing ◽  
Novel Genes

To gain more valuable genomic information about betalain biosynthesis, the full-length transcriptome of pitaya pulp from ‘Zihonglong’ (red pulp) and ‘Jinghonglong’ (white pulp) in four fruit developmental stages was analyzed using Single-Molecule Real-Time (SMRT) sequencing corrected by Illumina RNA-sequence (Illumina RNA-Seq). A total of 65,317 and 91,638 genes were identified in ‘Zihonglong’ and ‘Jinghonglong’, respectively. A total of 11,377 and 15,551 genes with more than two isoforms were investigated from ‘Zihonglong’ and ‘Jinghonglong’, respectively. In total, 156,955 genes were acquired after elimination of redundancy, of which, 120,604 genes (79.63%) were annotated, and 30,875 (20.37%) sequences without hits to reference database were probably novel genes in pitaya. A total of 31,169 and 53,024 simple sequence repeats (SSRs) were uncovered from the genes of ‘Zihonglong’ and ‘Jinghonglong’, and 11,650 long non-coding RNAs (lncRNAs) in ‘Zihonglong’ and 11,113 lncRNAs in ‘Jinghonglong’ were obtained herein. qRT-PCR was conducted on ten candidate genes, the expression level of six novel genes were consistent with the Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values. In conclusion, we firstly undertook SMRT sequencing of the full-length transcriptome of pitaya, and the valuable resource that was acquired through this sequencing facilitated the identification of additional betalain-related genes. Notably, a list of novel putative genes related to the synthesis of betalain in pitaya fruits was assembled. This may provide new insights into betalain synthesis in pitaya.

scholarly journals ­­Building a reference Transcriptome for Juniperus squamata (Cupressaceae) based on Single-molecule real-time sequencing

2021 ◽  
Author(s):  
Yufei Wang ◽  
Siyu Xie ◽  
Jialiang Li ◽  
Jieshi Tang ◽  
Tsam Ju ◽  
...  
Keyword(s):  
Real Time ◽  
Single Molecule ◽  
Evolutionary History ◽  
Full Length ◽  
Model Organisms ◽  
Rna Seq ◽  
Data Description ◽  
History Of ◽  
Simple Sequence

Abstract Objectives Cupressaceae is the second largest family of coniferous trees (Coniferopsida) with important economic and ecological values. However, like other conifers, the members of Cupressaceae have extremely large genome (>8 gigabytes), which limited the researches of these taxa. A high-quality transcriptome is an important resource for gene discovery and annotation for non-model organisms. Data descriptionJuniperus squamata, a tetraploid species which is widely distributed in Asian mountains, represents the largest genus, Juniperus, in Cupressaceae. Single-molecule real-time sequencing was used to obtain full-length transcriptome of Juniperus squamata. The full-length transcriptome was corrected with Illumina RNA-seq data from the same individual. A total of 47, 860 non-redundant full-length transcripts, N50 of which was 2, 839, were obtained. Simple sequence repeats for Juniperus squamata were also identified. This data presents the first comprehensive transcriptome characterization of Cupressaceae species, and provides an important reference for researches on the genomic evolutionary history of Cupressaceae plants and even conifers in the future.

Comparative analysis of transcriptional regulation of betalain biosynthesis based on SMRT sequencing of full-length transcriptome in two pitaya cultivars (red pulp and white pulp)

2019 ◽  
Author(s):  
Yawei Wu ◽  
Juan Xu ◽  
Xiumei Han ◽  
Guang Qiao ◽  
Kun yang ◽  
...  
Keyword(s):  
Single Molecule ◽  
Developmental Stages ◽  
Full Length ◽  
Reference Database ◽  
White Pulp ◽  
Rna Seq ◽  
Genomic Information ◽  
Smrt Sequencing ◽  
And Function ◽  
Red Pulp

Abstract Background: In order to gain more valuable genomic information involved in betalain biosynthesis, the full-length transcriptome of pitaya was analyzed using Single-Molecule Real-Time (SMRT) sequencing corrected by RNA-seq in the present study. Two pitaya cultivars, ‘Zihonglong’ (red pulp) and ‘Jinghonglong’ (white pulp) were selected to analyze betalain transcriptome in four fruit developmental stages. Results: A total of 65,317 and 91,638 genes coding proteins were identified in ‘Zihonglong’ and ‘Jinghonglong’, respectively. A total of 11,377 and 15,551 genes with more than two isoforms were investigated from ‘Zihonglong’ and ‘Jinghonglong’, respectively. Also, 156,955 genes were acquired after elimination of redundancy , of which, 120,604 genes (79.63%) were annotated, and 30,875 (20.37%) sequences without hits to reference database were probably novel genes in pitaya. Totally, 31,169 and 53,024 SSRs were uncovered from the genes of ‘Zihonglong’ and ‘Jinghonglong’, and 11,650 lncRNAs in ‘Zihonglong’ and 11,113 lncRNAs in ‘Jinghonglong’ were obtained herein. Further, 104 genes involved in betalain metabolism were identified, and HpCYP76AD4 and HpDODA probably responded to betalains biosynthesis. Conclusions: Conclusively, this is the first study to perform SMRT sequencing of the full-length transcriptome of pitaya, which provides a useful genomic clue for exploring the structure and function of genes in pitaya, particularly for betalain biosynthesis.

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