Analysis of alterations to the transcriptome of Loquat (Eriobotrya japonica Lindl.) under low temperature stress via de novo sequencing

Gong, Ronggao; Lai, Jing; Yang, Wei; Liao, Maoseng; Wang, Z H; Liang, Guo Lu

doi:10.4238/2015.august.14.6

Cited by 12 publications

(7 citation statements)

References 33 publications

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“…The rational classification of protein coding is critical to maximize the use of transcripts for functional research. The results of the COG analysis showed that the R function (general function prediction only) constituted the greatest proportion, followed by the K function (transcription), L function (replication, recombination and repair) and T function (signal transduction mechanisms),which was similar to the results reported by Gong [17]. This result indicated that the gene expression of loquat under low-temperature stress is related to the above functions and suggested that the use of transcriptome sequencing technology is an effective method for the study of functional genes.…”

Section: Plos Onesupporting

confidence: 87%

“…Current research on loquat has mainly focused on cell genetics [6,7], physiology and biochemistry [8,9], molecular markers [10], molecular clones [11,12], etc. Several transcriptome studies in loquat focused on flower bud differentiation [13], fruit development and ripening [14,15], and postharvest storage [16], research on transcriptome in cold stress of loquat is limited [17], little is known about its cold tolerance mechanisms. Previous studies have been performed using second generation sequencing technology, and many unigenes have been obtained, however, transcriptomic sequences using second generation sequencing technology may be misassembled without a high-quality genome sequence or full-length (FL) transcriptomic sequences available as a reference [18].…”

Section: Introductionmentioning

confidence: 99%

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Single-molecule real-time sequencing of the full-length transcriptome of loquat under low-temperature stress

Pan¹,

Wang²,

Tao³

et al. 2020

PLoS ONE

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In this study, third-generation full-length (FL) transcriptome sequencing was performed of loquat using single-molecule real-time(SMRT) sequencing from the pooled cDNA of embryos of young loquat fruit under different low temperatures (three biological replicates for treatments of 1˚C,-1˚C, and-3˚C, for 12 h or 24 h) and the control group(three biological replicates for treatments of room temperature), Illumina sequencing was used to correct FL transcriptome sequences. A total of 3 PacBio Iso-Seq libraries (1-2 kb, 2-3 kb and 3-6 kb) and 21 Illumina transcriptome libraries were constructed, a total of 13.41 Gb of clean reads were generated, which included 215,636 reads of insert (ROIs) and 121,654 FL, non-chimaric (FLNC) reads. Transcript clustering analysis of the FLNC reads revealed 76,586 consensus isoforms, and a total of 12,520 high-quality transcript sequences corrected with non-FL sequences were used for subsequent analysis. After the redundant reads were removed, 38,435 transcripts were obtained. A total of 27,905 coding DNA sequences (CDSs) were identified, and 407 long non-coding RNAs (lncRNAs) were ultimately predicted. Additionally, 24,832 simple sequence repeats (SSRs) were identified, and a total of 1,295 alternative splicing (AS) events were predicted. Furthermore, 37,993 transcripts were annotated in eight functional databases. This is the first study to perform SMRT sequencing of the FL transcriptome of loquat. The obtained transcriptomic data are conducive for further exploration of the mechanism of loquat freezing injury and thus serve as an important theoretical basis for generating new loquat material and for identifying new ways to improve loquat cold resistance.

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Section: Plos Onesupporting

confidence: 87%

Section: Introductionmentioning

confidence: 99%

Single-molecule real-time sequencing of the full-length transcriptome of loquat under low-temperature stress

Pan¹,

Wang²,

Tao³

et al. 2020

PLoS ONE

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“…These unigenes were used for BLASTX-algorithm based searches and annotations against the protein databases Nr, SwissPort, COG, KEGG, and GO. In total, 24,911 unigenes (34.62%) were annotated in sugar apple, which is much smaller than other fruit trees, such as pineapple (58.33%), mango (85%), and loquat (70.57%), and similar to the number annotated in manchurian walnut (39.92%) and “Bartlett” pears (32.8%) (Gong et al, 2015; Nham et al, 2015; Sherman et al, 2015; Hu et al, 2016; Liu and Fan, 2016). This indicated that the functions of a large portion of the genes of sugar apple have not yet been identified.…”

Section: Discussionmentioning

confidence: 92%

Transcriptome Analysis and Identification of Genes Associated with Floral Transition and Flower Development in Sugar Apple (Annona squamosa L.)

et al. 2016

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Sugar apple (Annona squamosa L.) is a semi-deciduous subtropical tree that progressively sheds its leaves in the spring. However, little information is available on the mechanism involved in flower developmental pattern. To gain a global perspective on the floral transition and flower development of sugar apple, cDNA libraries were prepared independently from inflorescent meristem and three flowering stages. Illumina sequencing generated 107,197,488 high quality reads that were assembled into 71,948 unigenes, with an average sequence length of 825.40 bp. Among the unigenes, various transcription factor families involved in floral transition and flower development were elucidated. Furthermore, a Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed that unigenes exhibiting differential expressions were involved in various phytohormone signal transduction events and circadian rhythms. In addition, 147 unigenes exhibiting sequence similarities to known flowering-related genes from other plants were differentially expressed during flower development. The expression patterns of 20 selected genes were validated using quantitative-PCR. The expression data presented in our study is the most comprehensive dataset available for sugar apple so far and will serve as a resource for investigating the genetics of the flowering process in sugar apple and other Annona species.

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“…Nevertheless, cold tolerance is an intricate biological process controlled by numerous factors. However, limited data were available regarding either physiological or genetic mechanisms that control the cold resistance ability of loquat, illustrating that the related regulatory mechanisms would accelerate cold-resistant breeding projects and enhance fruit production (Gong et al, 2015). Based on these, in this study, the physiological indices of different organs in loquat under cold stress were determined, and a comparative transcriptome analysis was performed against the rachis organs of two loquat varieties with distinct cold resistance to reveal the potential gene regulatory pathways, as well as the cross talk of genes controlling cold resistance in loquat.…”

Section: Discussionmentioning

confidence: 99%

Transcriptomic Analysis Reveals Potential Gene Regulatory Networks Under Cold Stress of Loquat (Eriobotrya japonica Lindl.)

Zhang

An²,

Zhang³

et al. 2022

Front. Plant Sci.

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Loquat (Eriobotrya japonica Lindl. ) is one of the most economically important evergreen fruit crops in China, while it often suffered the injury of cold stress in winter and earlier spring, and the annual yield loss of loquat fruits caused by cold or freezing stress was immeasurable. However, knowledge about the physiological response and molecular mechanism under cold stress is still limited. To investigate the potential regulation mechanism pre- and post-cold stress in loquat and the changes in physiological indicators, a comparative transcriptome analysis was performed against a cold-resistant cv. “Huoju” and a cold-sensitive cv. “Ninghaibai”. The results of physiological indicators related to cold resistance indicated that rachis was most sensitive to cold stress and was considered as the representative organ to directly evaluate cold resistance of loquat based on subordinate function analysis. Here, we compared the transcriptome profiles of rachis pre- and under cold stress in “Huoju” and “Ninghaibai”. A total of 4,347 and 3,513 differentially expressed genes (DEGs) were detected in “Ninghaibai” and “Huoju”, among which 223 and 166 were newly identified genes, respectively, most of them were functionally enriched in plant hormone signal transduction (Huoju: 142; Ninghaibai: 200), and there were higher plant hormone content and related DEG expression levels in “Huoju” than that of “Ninghaibai”. Moreover, a total of 3,309 differentially expressed transcription factors (DETFs) were identified, and some DEGs and DETFs were screened to be subjected to co-expression network analysis based on the gene expression profile data. Some candidate DEGs, including UDP-glycosyltransferase (UGT), glycosyltransferase (GT), sugar phosphate/phosphate translocator (SPT), sugar transport protein (STP), proline-rich receptor-like protein kinase (PERK), and peroxidise (POD), were significantly affected by cold stress, and the expression level of these genes obtained from real-time quantitative RT-PCR was consistent with the pattern of transcriptome profile, which suggested that these genes might play the vital roles in cold resistance of loquat. Our results provide an invaluable resource for the identification of specific genes and TFs and help to clarify gene transcription during the cold stress response of loquat.

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Analysis of alterations to the transcriptome of Loquat (Eriobotrya japonica Lindl.) under low temperature stress via de novo sequencing

Cited by 12 publications

References 33 publications

Single-molecule real-time sequencing of the full-length transcriptome of loquat under low-temperature stress

Single-molecule real-time sequencing of the full-length transcriptome of loquat under low-temperature stress

Transcriptome Analysis and Identification of Genes Associated with Floral Transition and Flower Development in Sugar Apple (Annona squamosa L.)

Transcriptomic Analysis Reveals Potential Gene Regulatory Networks Under Cold Stress of Loquat (Eriobotrya japonica Lindl.)

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