RNA-Seq analysis for transcriptome assembly, gene identification, and SSR mining in ginkgo (Ginkgo biloba L.)

Han, Shiming; Wu, Zhenjiang; Yang, Wei; Shi, Huazhong

doi:10.1007/s11295-015-0868-8

Cited by 28 publications

(21 citation statements)

References 54 publications

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“…For example, SSRs marker has been used to identify the position of the gene caused female sterile in wheat and soybean [25,26]. Severial studies about gymnosperms already focused on SSRs, such as Taxaceae, Pinus massoniana and Ginkgo biloba L. [64][65][66]. Similarly to the other gymnosperms [66], excluded the mono-nucleotide repeats, di-nucleotide repeats were the most abundant type, followed by tri-nucleotide repeats.…”

Section: Discussionmentioning

confidence: 99%

Single molecular real-time sequencing revealing the ovule abortion regulatory mechanisms in the female-sterile line of Pinus tabuliformis Carr.

Gong¹,

Han²,

Zhang³

et al. 2020

Preprint

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Background Ovule abortion is a common phenomenon in plants, which has an essential significance in seed production. The development of the female gametophyte (FG) is one of the crucial processes of the life cycle, and FG dysplasia is a significant cause contribute to ovule abortion in many species. However, because it is difficult to acquire the mutant about ovule development in gymnosperms, previous studies of the ovule and FG development are mainly focused on angiosperms, especially in Arabidopsis thaliana. Thus the investigation on this field of gymnosperms remains unclear. Results In this study, we investigated the transcriptome data of wild-type (female fertile line, FER) and natural ovule abortion mutant (female sterile line, STE) of Pinus tabuliformis Carr. to evaluate the mechanism of ovule abortion during the process of free nuclear mitosis (FNM). Using single molecule real-time (SMRT) sequencing and next-generation sequencing (NGS), we obtained 202,869 (FER), 197,977 (STE) mapped full-length non-chimeric (FLNC) reads and analyzed 18 cDNA libraries. Based on the SMRT sequencing, we found that both GO annotation and KEGG pathway terms results were similar in FER and STE. NGS analysis further showed altogether 99 differentially expressed genes (DEGs) with opposite expression patterns during the FNM process in FER and STE. According to SMRT sequencing, we found that the number of isoforms and alternative splicing (AS) patterns are variable between FER and STE. Moreover, 5,530 and 5,096 potential simple sequence repeats (SSRs) were identified in FER and STE, respectively. Functional annotation results demonstrated that genes involved in energy metabolism, signal transduction, cell division, and stress response were differentially expressed in different lines, 9 pairs of which were confirmed by quantitative real-time PCR. Conclusion Taken together, these results provide some new insights about the ovule abortion in gymnosperms and further reveal the regulatory mechanisms of ovule development.

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Section: Discussionmentioning

confidence: 99%

Single molecular real-time sequencing revealing the ovule abortion regulatory mechanisms in the female-sterile line of Pinus tabuliformis Carr.

Gong¹,

Han²,

Zhang³

et al. 2020

Preprint

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“…The ginkgo genome is of high scientific interest for its exclusive properties (Lin et al, 2011). The genomic research on G. biloba includes; (a) the identification of markers for sex identification -to support field planting of ginkgo (Liao et al, 2009;Yang et al, 2005), (b) cultivar identification -to contribute to the conservation, genetic diversity and mating patterns (Fan et al, 2004;Li and Zhang, 2013;Mei et al, 2014;Yan et al, 2006;Yan et al, 2009), (c) the high-throughput genomic research (Han et al, 2015;He et al, 2015;Lin et al, 2011) and (d) the comparison of the genomes of the species of G. biloba identified in Slovakia and abroad, characterization of morphological gender differences, and peculiarities within the species (Ražná et al, 2014;Ražná and Hrubík, 2016). Šmarda et al (2016) observed the polyploidy of the ginkgo genome, which is quite unusual in gymnosperms.…”

Section: Introductionmentioning

confidence: 99%

Ecologically conditioned imprinting of miRNA-based profiles of Ginkgo biloba L. growing in Slovakia

et al. 2019

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Ražná, K., Žiarovská, J., Hrubík, P., Batyaneková, V., Vargaová, A., 2019. Ecologically conditioned imprinting of miRNA-based profiles of Ginkgo biloba L. growing in Slovakia. Folia Oecologica, 46: 54-62.Ginkgo biloba L. is characterized by its high level of resistance to climatic conditions, diseases, and pests. In Slovakia, there is a rich collection of genetic resources of ginkgo consisting of 288 trees growing in 103 locations and providing valuable biological material for scientific research. There have been documented 45 trees of ginkgo older than 100 years (ranging from 112 to 242 years of age). Their dendrometrical parameters were recorded. For genomic imprinting, three types of microRNA-based markers were selected; highly conserved gb-miR160, moderately conserved gb-miR482 and the species-specific gb-miR75. The most efficient one can be considered the marker gb-miR482 with its genotype-unique miRNA profiles probably related to this marker functioning in the defence mechanisms of the ginkgo species. Unique miRNA loci were recorded in genomes of young ginkgo trees. We found that, by selecting the appropriate microRNA-based markers, it is possible to characterize the ginkgo genome in the context of microclimatic conditions.

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“…mRNA sequencing (RNA-Seq) is a next-generation sequencing technology [12] [13] [14] [15] that has been used widely to authenticate and quantify normal and rare transcripts, and to provide transcript sequential structure information of specific samples [16] [17] in species without a reference genome. The recent application of RNA-Seq to G. biloba aseptic seedlings identified a gene that encoded chalcone isomerase (GbCHI1), one of the key enzymes in the flavonoid biosynthesis pathway, that exhibited differences in the protein sequence compared with a previously identified GbCHI [18]. Transcriptome sequencing of G. biloba kernels revealed 66 unigenes that were found to be responsible for terpenoid backbone biosynthesis [19].…”

Section: Introductionmentioning

confidence: 99%

RNA-Seq and Bulked Segregant Analysis of Genes Related to High Growth in <i>Ginkgo biloba</i> Half-Sibling Families

Tang¹,

Men²,

Zhang³

et al. 2019

AJPS

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The lifetime of G. biloba is very long, and its growth is relatively slow. However, little is known about growth-related genes in this species. We combined mRNA sequencing (RNA-Seq) with bulked segregant analysis (BSA) to fine map significant agronomic trait genes by developing polymorphism molecular markers at the transcriptome level. In this study, transcriptome sequencing of high growth (GD) and low growth (BD) samples of G. biloba half-sib families was performed. After assembling the clean reads, 601 differential expression genes were detected and 513 of them were assigned functional annotations. Single nucleotide polymorphism (SNP) analysis identified SNPs associated with 119 genes in the GD and BD groups; 58 of these genes were annotated. Two Homeobox-leucine zipper protein genes were up-regulated in the GD group compared with the BD group; therefore, these are very likely related to high growth of G. biloba. This study provides molecular level data that could be used for seed selection of high growth G. biloba half-sib families for future breeding programs.

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RNA-Seq analysis for transcriptome assembly, gene identification, and SSR mining in ginkgo (Ginkgo biloba L.)

Cited by 28 publications

References 54 publications

Single molecular real-time sequencing revealing the ovule abortion regulatory mechanisms in the female-sterile line of Pinus tabuliformis Carr.

Single molecular real-time sequencing revealing the ovule abortion regulatory mechanisms in the female-sterile line of Pinus tabuliformis Carr.

Ecologically conditioned imprinting of miRNA-based profiles of Ginkgo biloba L. growing in Slovakia

RNA-Seq and Bulked Segregant Analysis of Genes Related to High Growth in <i>Ginkgo biloba</i> Half-Sibling Families

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RNA-Seq analysis for transcriptome assembly, gene identification, and SSR mining in ginkgo (Ginkgo biloba L.)

Cited by 28 publications

References 54 publications

Single molecular real-time sequencing revealing the ovule abortion regulatory mechanisms in the female-sterile line of Pinus tabuliformis Carr.

Single molecular real-time sequencing revealing the ovule abortion regulatory mechanisms in the female-sterile line of Pinus tabuliformis Carr.

Ecologically conditioned imprinting of miRNA-based profiles of Ginkgo biloba L. growing in Slovakia

RNA-Seq and Bulked Segregant Analysis of Genes Related to High Growth in &lt;i&gt;Ginkgo biloba&lt;/i&gt; Half-Sibling Families

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RNA-Seq and Bulked Segregant Analysis of Genes Related to High Growth in <i>Ginkgo biloba</i> Half-Sibling Families