De novo transcriptome assembly and EST-SSR markers development for Zelkova schneideriana Hand.-Mazz. (Ulmaceae)

Wang, Lingdan; Zhang, Riqing; Geng, Maolin; Qin, Yufeng; Liu, Hailong; Li, Lingli; Li, Mimi

doi:10.1007/s13205-021-02968-5

Cited by 3 publications

(3 citation statements)

References 40 publications

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“…We have revealed for the first time the distribution characteristics of EST-SSRs in the All UniTransModels, identifying a total of 8032 potential EST-SSR loci in 5530 pseudogene transcripts and successfully designing 5709 primer pairs (distributed among 4354 Unigenes). The frequency of EST-SSR occurrence in reeds was as high as 51.65%, which is much higher than species such as Arachis hypogaea L (7.71%) [ 62 ], Zelkova schneideriana Hand.-Mazz (6.04%) [ 63 ], Elymus sibiricus (6.55%) [ 64 ], Bromus cathartics [ 65 ], Carex L (24.11%) [ 66 ]. Among the single nucleotide repeat motifs, the A/T repeats (2,556) were 2.21 times higher than the C/G repeats (1,156), which may be due to the higher number of polyA in the P. australis transcript.…”

Section: Discussionmentioning

confidence: 99%

De novo full-length transcriptome analysis of two ecotypes of Phragmites australis (swamp reed and dune reed) provides new insights into the transcriptomic complexity of dune reed and its long-term adaptation to desert environments

Cui

Qiu

et al. 2023

BMC Genomics

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Background The extremely harsh environment of the desert is changing dramatically every moment, and the rapid adaptive stress response in the short term requires enormous energy expenditure to mobilize widespread regulatory networks, which is all the more detrimental to the survival of the desert plants themselves. The dune reed, which has adapted to desert environments with complex and variable ecological factors, is an ideal type of plant for studying the molecular mechanisms by which Gramineae plants respond to combinatorial stress of the desert in their natural state. But so far, the data on the genetic resources of reeds is still scarce, therefore most of their research has focused on ecological and physiological studies. Results In this study, we obtained the first De novo non-redundant Full-Length Non-Chimeric (FLNC) transcriptome databases for swamp reeds (SR), dune reeds (DR) and the All of Phragmites australis (merged of iso-seq data from SR and DR), using PacBio Iso-Seq technology and combining tools such as Iso-Seq3 and Cogent. We then identified and described long non-coding RNAs (LncRNA), transcription factor (TF) and alternative splicing (AS) events in reeds based on a transcriptome database. Meanwhile, we have identified and developed for the first time a large number of candidates expressed sequence tag-SSR (EST-SSRs) markers in reeds based on UniTransModels. In addition, through differential gene expression analysis of wild-type and homogenous cultures, we found a large number of transcription factors that may be associated with desert stress tolerance in the dune reed, and revealed that members of the Lhc family have an important role in the long-term adaptation of dune reeds to desert environments. Conclusions Our results provide a positive and usable genetic resource for Phragmites australis with a widespread adaptability and resistance, and provide a genetic database for subsequent reeds genome annotation and functional genomic studies.

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Section: Discussionmentioning

confidence: 99%

De novo full-length transcriptome analysis of two ecotypes of Phragmites australis (swamp reed and dune reed) provides new insights into the transcriptomic complexity of dune reed and its long-term adaptation to desert environments

Cui

Qiu

et al. 2023

BMC Genomics

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“…The Actin2 gene was used as an internal control. The reactions were carried out with a final volume of 20 µL as reported earlier [6]. The reactions were carried out on a Rotor-Gene 6000 machine (Qiagen, Shanghai, China).…”

Section: Qrt-pcr Analysesmentioning

confidence: 99%

“…The observable differences in growth, plant height, and branching points in J and H indicate the possibility of different growth regulation mechanisms. To date, only limited data are available, as the major focus of the research has been on in-vitro regeneration [4], evolution [5], and the development of molecular markers for genetic diversity studies [6,7]. However, some earlier investigations on other seedlings and saplings of Z. schneideriana have shown that the trees can differ in growth traits and such traits are moderately to highly heritable [8].…”

Section: Introductionmentioning

confidence: 99%

Comparative Transcriptome Sequencing and Endogenous Phytohormone Content of Annual Grafted Branches of Zelkova schneideriana and Its Dwarf Variety HenTianGao

Huang,

Jin,

Lin

et al. 2023

IJMS

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Zelkova schneideriana is a fast-growing tree species endemic to China. Recent surveys and reports have highlighted a continued decline in its natural populations; therefore, it is included in the Red List of Threatened Species by The International Union for Conservation of Nature. A new variety “HenTianGao” (H) has been developed with smaller plant height, slow growth, and lower branching points. In this study, we attempted to understand the differences in plant height of Z. schneideriana (J) and its dwarf variety H. We determined the endogenous hormone content in the annual grafted branches of both J and H. J exhibited higher gibberellic acid (GA)-19 and trans-Zeatin (tZ) levels, whereas H had higher levels of indole-3-acetic acid (IAA) catabolite 2-oxindole-3-acetic acid (OxIAA), IAA-Glu conjugate, and jasmonic acid (JA) (and its conjugate JA-Ile). The transcriptome comparison showed differential regulation of 20,944 genes enriched in growth and development, signaling, and metabolism-related pathways. The results show that the differential phytohormone level (IAA, JA, tZ, and GA) was consistent with the expression of the genes associated with their biosynthesis. The differences in relative OxIAA, IAA-Glu, GA19, trans-Zeatin, JA, and JA-Ile levels were linked to changes in respective signaling-related genes. We also observed significant differences in the expression of cell size, number, proliferation, cell wall biosynthesis, and remodeling-related genes in J and H. The differences in relative endogenous hormone levels, expression of biosynthesis, and signaling genes provide a theoretical basis for understanding the plant height differences in Z. schneideriana.

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Genetic diversity and DNA fingerprinting of Hemerocallis spp. accessions based on EST-SSR markers

Wang

Liu

Zhang

et al. 2023

Genet Resour Crop Evol

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De novo transcriptome assembly and EST-SSR markers development for Zelkova schneideriana Hand.-Mazz. (Ulmaceae)

Cited by 3 publications

References 40 publications

De novo full-length transcriptome analysis of two ecotypes of Phragmites australis (swamp reed and dune reed) provides new insights into the transcriptomic complexity of dune reed and its long-term adaptation to desert environments

De novo full-length transcriptome analysis of two ecotypes of Phragmites australis (swamp reed and dune reed) provides new insights into the transcriptomic complexity of dune reed and its long-term adaptation to desert environments

Comparative Transcriptome Sequencing and Endogenous Phytohormone Content of Annual Grafted Branches of Zelkova schneideriana and Its Dwarf Variety HenTianGao

Genetic diversity and DNA fingerprinting of Hemerocallis spp. accessions based on EST-SSR markers

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