SMRT sequencing analysis reveals the full-length transcripts and alternative splicing patterns in <i>Ananas comosus</i> var. <i>bracteatus</i>

Ma, Jun; Xiang, Yixuan; Xiong, Yingyuan; Lin, Zhen Yuan; Xue, Ying; Mao, Meiqin; Sun, Lina; Zhou, Yujue; Li, Xi; Huang, Zhuo

doi:10.7717/peerj.7062

Cited by 12 publications

(15 citation statements)

References 43 publications

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“…Similarly, in tomato, moso bamboo, and A. comosus var. bracteatus, researchers have reported that AS genes and non-AS genes have no differences in splicing site selection (Zhao et al, 2018;Clark et al, 2019;Ma et al, 2019). Moreover, we found that short exons tended to be skipped, while short introns tended to be retained ( Figures 10A, B).…”

Section: Discussionmentioning

confidence: 52%

“…These results are consistent with findings obtained for tomato and Ananas comosus var. bracteatus (Clark et al, 2019;Ma et al, 2019).…”

Section: Differences Between As Genes and Non-as Genesmentioning

confidence: 99%

“…Although the functions of alternative splicing in animals and plants are similar, some differences exist between them in some aspects. For example, intron retention (IR) has been reported to be the most frequent AS event in plants, whereas exon skipping (ES) is the major type in humans and animals (Xu et al, 2002;Wang et al, 2008;Ruan et al, 2018;Ma et al, 2019;Wang Z. et al, 2019). The Suppressor of Morphological defects on Genitalia (SMG) gene family (SMG 1-7), which plays an important role in the AS-coupled-NMD pathway, has been widely reported in animals; however, no SMG 5 and SMG 6 paralogs have been identified in plants.…”

Section: Introductionmentioning

confidence: 99%

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Alternative Splicing Enhances the Transcriptome Complexity of Liriodendron chinense

Tu¹,

Shen²,

Wen³

et al. 2020

Front. Plant Sci.

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Alternative splicing (AS) plays pivotal roles in regulating plant growth and development, flowering, biological rhythms, signal transduction, and stress responses. However, no studies on AS have been performed in Liriodendron chinense, a deciduous tree species that has high economic and ecological value. In this study, we used multiple tools and algorithms to analyze transcriptome data derived from seven tissues via hybrid sequencing. Although only 17.56% (8,503/48,408) of genes in L. chinense were alternatively spliced, these AS genes occurred in 37,844 AS events. Among these events, intron retention was the most frequent AS event, producing 1,656 PTCcontaining and 3,310 non-PTC-containing transcripts. Moreover, 183 long noncoding RNAs (lncRNAs) also underwent AS events. Furthermore, weighted gene coexpression network analysis (WGCNA) revealed that there were great differences in the activities of transcription and post-transcriptional regulation between pistils and leaves, and AS had an impact on many physiological and biochemical processes in L. chinense, such as photosynthesis, sphingolipid metabolism, fatty acid biosynthesis and metabolism. Moreover, our analysis showed that the features of genes may affect AS, as AS genes and non-AS genes had differences in the exon/intron length, transcript length, and number of exons/introns. In addition, the structure of AS genes may impact the frequencies and types of AS because AS genes with more exons or introns tended to exhibit more AS events, and shorter introns tended to be retained, whereas shorter exons tended to be skipped. Furthermore, eight AS genes were verified, and the results were consistent with our analysis. Overall, this study reveals that AS and gene interaction are mutual-on one hand, AS can affect gene expression and translation, while on the other hand, the structural characteristics of the gene can also affect AS. This work is the first to comprehensively report on AS in L. chinense, and it can provide a reference for further research on AS in L. chinense.

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Section: Discussionmentioning

confidence: 52%

“…These results are consistent with findings obtained for tomato and Ananas comosus var. bracteatus (Clark et al, 2019;Ma et al, 2019).…”

Section: Differences Between As Genes and Non-as Genesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Alternative Splicing Enhances the Transcriptome Complexity of Liriodendron chinense

Tu¹,

Shen²,

Wen³

et al. 2020

Front. Plant Sci.

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“…LncRNAs are largely involved in regulating plant development and growth, secondary metabolism, and the plant stress response 44 . Recently, an increasing number of studies have focused on the functions of lncRNAs in plants such as in red pineapple 45 and hot pepper 46 . However, no lncRNAs from Rhododendron have been reported.…”

Section: Searching Item Numbersmentioning

confidence: 99%

Single-molecule long-read sequencing of the full-length transcriptome of Rhododendron lapponicum L.

Jia

Tang

Mei

et al. 2020

Sci Rep

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Rhododendron lapponicum L. is a familiar ornamental plant worldwide with important ornamental and economic value. However, a full-length R. lapponicum transcriptome is still lacking. in the present study, we used the Pacific Biosciences single-molecule real-time sequencing technology to generate the R. lapponicum transcriptome. A total of 346,270 full-length non-chimeric reads were generated, from which we obtained 75,002 high-quality full-length transcripts. We identified 55,255 complete open reading frames, 7,140 alternative splicing events and 2,011 long non-coding RNAs. In gene annotation analyses, 71,155, 33,653, 30,359 and 31,749 transcripts were assigned to the Nr, GO, COG and KEGG databases, respectively. Additionally, 3,150 transcription factors were detected. KEGG pathway analysis showed that 96 transcripts were identified coding for the enzymes associated with anthocyanin synthesis. Furthermore, we identified 64,327 simple sequence repeats from 45,319 sequences, and 150 pairs of primers were randomly selected to develop SSR markers. this study provides a large number of full-length transcripts, which will facilitate the further study of the genetics of R. lapponicum.Rhododendron is the largest genus in Ericaceae, with more than 1000 species of woody plants, either evergreen or deciduous 1 . Rhododendron species are widely cultivated around the world ranging from tropical to polar climates, and serve as a potential genetic resource for the development of new plant cultivars adapted to different environmental conditions 2 . Rhododendron is a familiar ornamental plant worldwide, and is decorative shrub with beautiful flowers that are widespread around the world. There are a remarkably broad range of rhododendron flower colours, including red, white, yellow, and green and so on. Rhododendron lapponicum L., a Rhododendron species found in subarctic regions around the world, is a common ornamental plant worldwide 3 . Recent advances in sequencing technology have facilitated genome and transcriptome studies in many species. However, genome and transcriptome sequencing in R. lapponicum has lagged behind that in other species, and information about the sequence and structure of its genes is limited. Therefore, the generation of a transcriptome data may establish a very important molecular biology basis for the research of R. lapponicum.The transcriptome reflects the number and type of genes expressed in different cell types and reveals underlying metabolic pathways and genetic mechanisms 4 . Transcriptome sequencing is an efficient and feasible approach for generating a large amount of sequence data, and a large number of cDNA sequences provides a useful resource for genomic and genetic research 5-9 . Thus, third-generation long-read transcriptome sequencing platforms such as the Pacific Biosciences (PacBio), Nanopore and Moleculo platforms were developed. Recently, PacBio single-molecule real-time (SMRT) sequencing technology has served as a better alternative for obtaining full-length transcripts 10,11 . The ...

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“…The assembly genome of Huagu11 had the highest continuity than previous genomes, which should be attributed to the use of the SMRT sequencing and Hi-C [ 24 ]. The genome of Yugu1 was based on the sanger sequencing technology [ 9 ], while Zhanggu and TT8 were based on the whole genome shotgun–next-generation sequencing strategy.…”

Section: Resultsmentioning

confidence: 99%

De novo genome assembly of a foxtail millet cultivar Huagu11 uncovered the genetic difference to the cultivar Yugu1, and the genetic mechanism of imazethapyr tolerance

Wang

Lan

et al. 2021

BMC Plant Biol

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Background Setaria italica is the second-most widely planted species of millets in the world and an important model grain crop for the research of C4 photosynthesis and abiotic stress tolerance. Through three genomes assembly and annotation efforts, all genomes were based on next generation sequencing technology, which limited the genome continuity. Results Here we report a high-quality whole-genome of new cultivar Huagu11, using single-molecule real-time sequencing and High-throughput chromosome conformation capture (Hi-C) mapping technologies. The total assembly size of the Huagu11 genome was 408.37 Mb with a scaffold N50 size of 45.89 Mb. Compared with the other three reported millet genomes based on the next generation sequencing technology, the Huagu11 genome had the highest genomic continuity. Intraspecies comparison showed about 94.97 and 94.66% of the Yugu1 and Huagu11 genomes, respectively, were able to be aligned as one-to-one blocks with four chromosome inversion. The Huagu11 genome contained approximately 19.43 Mb Presence/absence Variation (PAV) with 627 protein-coding transcripts, while Yugu1 genomes had 20.53 Mb PAV sequences encoding 737 proteins. Overall, 969,596 Single-nucleotide polymorphism (SNPs) and 156,282 insertion-deletion (InDels) were identified between these two genomes. The genome comparison between Huagu11 and Yugu1 should reflect the genetic identity and variation between the cultivars of foxtail millet to a certain extent. The Ser-626-Aln substitution in acetohydroxy acid synthase (AHAS) was found to be relative to the imazethapyr tolerance in Huagu11. Conclusions A new improved high-quality reference genome sequence of Setaria italica was assembled, and intraspecies genome comparison determined the genetic identity and variation between the cultivars of foxtail millet. Based on the genome sequence, it was inferred that the Ser-626-Aln substitution in AHAS was responsible for the imazethapyr tolerance in Huagu11. The new improved reference genome of Setaria italica will promote the genic and genomic studies of this species and be beneficial for cultivar improvement.

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SMRT sequencing analysis reveals the full-length transcripts and alternative splicing patterns in Ananas comosus var. bracteatus

Cited by 12 publications

References 43 publications

Alternative Splicing Enhances the Transcriptome Complexity of Liriodendron chinense

Alternative Splicing Enhances the Transcriptome Complexity of Liriodendron chinense

Single-molecule long-read sequencing of the full-length transcriptome of Rhododendron lapponicum L.

De novo genome assembly of a foxtail millet cultivar Huagu11 uncovered the genetic difference to the cultivar Yugu1, and the genetic mechanism of imazethapyr tolerance

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