Full-length RNA sequencing reveals unique transcriptome composition in bermudagrass

Zhang, Bing; Liu, Jianxiu; Wang, Xiaoshan; Wei, Zhenwu

doi:10.1016/j.plaphy.2018.08.039

Cited by 49 publications

(35 citation statements)

References 53 publications

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“…Development of de novo assembly expands the applicability of second generation RNA sequencing especially to non-model organisms without a proper reference genome, such as A. lucorum [32]. However, the next-generation RNA sequencing transcriptome analyses in species without reference genome sequences often encounter assembly problems [35]. Therefore, a high-confidence transcriptome atlas is needed to help us better understand and control this important pest species.…”

Section: Discussionmentioning

confidence: 99%

Analysis of Differentially Expressed Transcripts in Apolygus lucorum (Meyer-Dür) Exposed to Different Temperature Coefficient Insecticides

Liu

Dou

et al. 2020

IJMS

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The existence of a temperature effect of insecticides frustrated the control of the green plant bug Apolygus lucorum (Meyer-Dür). Previous studies mostly focused on the application of insecticides, but the underlying mechanism remains incompletely understood. Here, we report a transcriptome profiling of A. lucorum treated by three kinds of temperature coefficient insecticides (TCIs) (positive TCI: imidacloprid, negative TCI: b-cypermethrin and non-effect TCI: phoxim) at 15 °C, 25 °C and 35 °C by using next- and third-generation RNA-Seq methods. A total of 34,739 transcripts were annotated from 277.74 Gb of clean data. There were more up-regulated transcripts than down-regulated transcripts in all three kinds of TCI treatments. Further Venn diagrams indicate the regulatory transcripts and regulatory modes were different at the three temperatures. The responses to imidacloprid involved more detox and stress response transcripts such as cytochrome P450 (CYP450), carboxylesterase (CarE) and catalase (CAT) at 35 °C, which was the case for beta-cypermethrin at 15 °C. UDP-glucuronyltransferase (UGT) and heat shock protein (HSP) transcripts were heavily involved, and thus deserve particular note in the temperature effect of insecticides. This high-confidence transcriptome atlas provides improved gene information for further study on the insecticide temperature effect related physiological and biochemical processes of A. lucorum.

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Section: Discussionmentioning

confidence: 99%

Analysis of Differentially Expressed Transcripts in Apolygus lucorum (Meyer-Dür) Exposed to Different Temperature Coefficient Insecticides

Liu

Dou

et al. 2020

IJMS

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“…[38], Cynodon dactylon L. Pers. [39], Camellia sinensis L. O. Ktze. [40], and Cassia obtusifolia L. [41].…”

Section: Introductionmentioning

confidence: 99%

Single-Molecule Long-Read Sequencing of Avocado Generates Microsatellite Markers for Analyzing the Genetic Diversity in Avocado Germplasm

Zang

Tan

et al. 2019

Agronomy

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Avocado (Persea americana Mill.) is an important fruit crop commercially grown in tropical and subtropical regions. Despite the importance of avocado, there is relatively little available genomic information regarding this fruit species. In this study, we functionally annotated the full-length avocado transcriptome sequence based on single-molecule real-time sequencing technology, and predicted the coding sequences (CDSs), transcription factors (TFs), and long non-coding RNA (lncRNA) sequences. Moreover, 76,777 simple sequence repeat (SSR) loci detected among the 42,096 SSR-containing transcript sequences were used to develop 149,733 expressed sequence tag (EST)-SSR markers. A subset of 100 EST-SSR markers was randomly chosen for an analysis that detected 15 polymorphicEST-SSR markers, with an average polymorphism information content of 0.45. These 15markers were able to clearly and effectively characterize46 avocado accessions based on geographical origin. In summary, our study is the first to generate a full-length transcriptome sequence and develop and analyze a set of EST-SSR markers in avocado. The application of third-generation sequencing techniques for developing SSR markers is a potentially powerful tool for genetic studies.

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“…With the capability to obtain full-length RNA sequences (Isoseq), PacBio Isoseq has been used for the discovery of new genes, isoforms, and alternative splicing events; this technology is improving genome annotation in crop species such as maize (Zea mays), rice (Oryza sativa), sugarcane (Saccharum o cinarum), and sorghum (Sorghum bicolor) (Wang et al, 2016;Hoang et al, 2017;McCormick et al, 2018;Zhang et al, 2019). In turfgrass and ground cover related genetics research, PacBio Isoseq has been used to study the transcriptome and phylogeny of bermudagrass (Cynodon dactylon) and red clover (Trifolium pratense) (Chao et al, 2018;Zhang et al, 2018). Due to the highly outcrossing and polyploid nature of F. brevipila, PacBio isoform sequencing is ideal for generating a reference transcriptome for plant breeding and genetics research.…”

Section: Introductionmentioning

confidence: 99%

Building a Reference Transcriptome for the Hexaploid Hard Fescue Turfgrass (Festuca brevipila) Using a Combination of PacBio Isoseq and Illumina Sequencing

Qiu

Yang

Hirsch

et al. 2020

Preprint

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Background: Hard fescue (Festuca brevipila Tracey, 2n=6x=42) is a cool season turfgrass with a fine leaf texture that performs well under low-input management. Breeding and genetics studies of F. brevipila have been limited due to the complexity of its hexaploid genome. To advance our knowledge of F. brevipila genomics, we used PacBio isoform sequencing to develop a reference transcriptome for this species. Results: Here, we report the F. brevipila reference transcriptome generated from root, crown, leaf, and inflorescence tissues. We obtained 59,510 full-length transcripts, of which 38,556 were non-redundant full-length transcripts. The longest and shortest transcripts were 11,487 and 58 bp, respectively. Distribution of synonymous distances among paralogs within F. brevipila suggested highly similar subgenomes that are difficult to distinguish from sequencing errors. To evaluate the phylogenetic relationships among F. brevipila and close relatives, we sequenced three additional transcriptomes using closely related species on an Illumina platform. The results of our phylotranscriptomic analysis supported the close relationships among F. brevipila (6x), Festuca ovina (4x), Festuca ovina subsp. ovina (2x), and Festuca valesiaca (2x), with high levels of discordance among gene trees. Conclusions: Overall, the F. brevipila PacBio Isoseq reference transcriptome provided the foundation for transcriptome studies and allowed breeders a resource for gene discovery in this important turfgrass species.

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Full-length RNA sequencing reveals unique transcriptome composition in bermudagrass

Cited by 49 publications

References 53 publications

Analysis of Differentially Expressed Transcripts in Apolygus lucorum (Meyer-Dür) Exposed to Different Temperature Coefficient Insecticides

Analysis of Differentially Expressed Transcripts in Apolygus lucorum (Meyer-Dür) Exposed to Different Temperature Coefficient Insecticides

Single-Molecule Long-Read Sequencing of Avocado Generates Microsatellite Markers for Analyzing the Genetic Diversity in Avocado Germplasm

Building a Reference Transcriptome for the Hexaploid Hard Fescue Turfgrass (Festuca brevipila) Using a Combination of PacBio Isoseq and Illumina Sequencing

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