Characterization of ESTs from black locust for gene discovery and marker development

Wang, J X; Lü, Caixia; Yuan, Cunquan; Cui, Binbin; Qiu, Qiongfen; Sun, Peng; Hu, Ruiyang; Wu, Dongyang; Sun, Yuze; Li, Yun

doi:10.4238/2015.october.19.12

Cited by 10 publications

(9 citation statements)

References 30 publications

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“…In total, 991 miRNAs containing 671 novel miRNAs were obtained. Compared to the previous study of R. pseudoacacia, the sequencing results obtained in this study provide longer unigenes, and the overall results are better than before [45][46][47]. Overall 131,359 (74.69%) of the identified unigenes were successfully annotated using BLAST searches of the public Nr, Nt, Swiss-prot, GO, COG and KEGG databases, given the absence of genomic information on R. seudoacasia; 86 (26.88%) out of 320 known miRNAs were detected based on 82 other species' miRNAs from miRBase 21.0 (Supporting Table 9).…”

Section: Discussioncontrasting

confidence: 57%

Integrated analysis of the physiology, RNA, and microRNA involved in black locust (Robinia pseudoacacia) rejuvenation

Zhang

Sun

Han

et al. 2019

Preprint

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Background Rejuvenation is a key process that enables perennial woody plants to regain growth potential. In Robinia pseudoacacia plantations, natural root sprouting individuals provide good material for studying the rejuvenation of woody plants. However, the physiological differences and molecular mechanisms underlying black locust rejuvenation remain unclear. In this study, we compared the physiological conditions and molecular responses of rejuvenated individuals and mother trees. Results Our analysis of leaf structures and physiological indices showed that the epidermis thickness, leaf thickness and leaf-tissue tightness of rejuvenated individuals were less than those of mother trees. The soluble-sugar content and total SOD activity of rejuvenated individuals were also lower than those of mother trees. The younger the rejuvenated individuals were, the lower the ABA content, ABA/ZT and GA3/ZT in the leaves. The ZT content increased with decreasing age of rejuvenated individuals. Using high-throughput sequencing strategies, the mRNA and miRNA involved in the rejuvenation of black locust were identified. RNA-seq identified 175,862 unigenes by de novo transcript assembly. Of those, 4,727 differentially expressed genes were identified based on clean reads mapped to the assembled transcriptome for gene expression analysis(fold change≥2 or ≤0.5 and q-value≤0.05). These genes were enriched to 53 gene ontology(GO) terms and 20 KEGG pathways (FDR≤0.01). Among these were a major pathway related to flavone and flavonol biosynthesis. High-throughput miRNA sequencing identified a total of 991 miRNAs, including 671 novel miRNAs. Furthermore, 262 known and 625 novel differentially expressed miRNAs were identified(fold change≥1.5 or ≤0.67 and p≤0.05). The main functions identified in the GO analysis of the target predictions overlapped with differentially expressed genes derived from RNA-seq. KEGG pathway enrichment showed that circadian rhythm-fly and signaling pathways regulating pluripotency of stem cells attracted considerable attention during rejuvenation. Conclusion Our study revealed physiological differences between rejuvenated individuals and mother trees of R. pseudoacacia. Differential genes between mother trees and rejuvenated individuals may vary according to the tree ages, but miRNAs may play a key regulatory role in rejuvenation. The same genotype system composed of root germinating individuals and mother-tree individuals provides a solid starting point for further elucidation of the rejuvenation of woody plants.

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Section: Discussioncontrasting

confidence: 57%

Integrated analysis of the physiology, RNA, and microRNA involved in black locust (Robinia pseudoacacia) rejuvenation

Zhang

Sun

Han

et al. 2019

Preprint

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“…However, studies have shown that dinucleotide repeats are the most predominant repeat motif type in many plants, especially in dicots such as Arabidopsis, peanut, soybean, bean and grape [38]. The result contrasts with both Wang et al (2015) [18] and Guo et al (2017) [19]. They identified that tri-nucleotide repeats were the most abundant repeat motif type in black locust.…”

Section: Frequency and Characteristics Of Ssrs In Black Locust Est Sementioning

confidence: 83%

“…For black locust, Lian et al (2002Lian et al ( , 2004 [15,16] and Mishima et al (2009) [17] have developed a total of 21 SSR markers. In addition, Wang et al (2015) [18] and Guo et al (2017) [19] have conduct a preliminary research on SSR loci in the EST sequences and a novel set of EST-SSR markers have been developed. However, compared with other species, the relatively limited number of efficient EST-SSR markers for black locust greatly obstructs its application to breeding research.…”

Section: Introductionmentioning

confidence: 99%

Development and Application of EST-SSR Markers for DNA Fingerprinting and Genetic Diversity Analysis of the Main Cultivars of Black Locust (Robinia pseudoacacia L.) in China

Dong

Sun

Zhao

et al. 2019

Forests

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Black locust (Robinia pseudoacacia L.) is an economically and ecologically important tree species which is used for pillar construction, honey production and soil improvement. More EST-SSR (Expressed sequence tag simple sequence repeat) markers of black locust can be used as a complement and improvement of Genomic-SSR markers for the identification of the function of gene and the construction of genetic map. Additionally, currently there is no simple method for identifying black locust cultivars. In this study, we obtained 2702 unigenes from 3095 expressed sequence tags (ESTs) from the National Center of Biotechnology Information (NCBI) database to identify simple sequence repeats (SSRs) in R. pseudoacacia samples. A total of 170 SSR loci were found to be distributed in 162 non-redundant sequences with a frequency of 6.29%. Dinucleotide repeats were the most predominant types among microsatellites (62.35%), followed by tri-nucleotide repeats (25.88%); the remaining SSRs accounted for less than 12%. The repeat motifs AG/TC (29.25%) and CT/GA (29.25%) were the most abundant among dinucleotides, and AAT/TTA (15.91%) was the most common among tri-nucleotides. A total of 62 primer pairs were designed to screen polymorphic and stable SSR loci. The resulting 25 EST-SSR markers capable of amplifying polymorphic, stable, and repeatable products. Eight newly developed EST-SSR markers and four published SSR markers were selected for DNA fingerprinting and genetic diversity analysis of the 123 main R. pseudoacacia cultivars in China. The 12 SSR loci amplified 102 alleles, with an average number of alleles per locus of 8.5 (range 4-15). The average polymorphism information content at the 12 SSR loci for the 123 cultivars was 0.670 (range 0.427-0.881). The 123 cultivars clustered into six main groups based on similarity coefficients, with most cultivars in one subgroup. Fingerprinting was performed using eight SSR markers; 110 black locust cultivars were distinguished. The results of this study increase the availability of EST-SSR markers in black locust and make it a simple method for checking the collection, the certification, and the correct attribution of clones and cultivars.

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“…Progress in novel gene discovery and molecular breeding in crop plants was under processing with the advent of high throughput technologies and the utilization of bioinformatics methodologies. 5,6 Transcriptome sequencing has, however caused a significant upshot in the expressed sequence tags (ESTs) collections in several plant species, including the non-model plant species. 7 The ESTs, which are generated by large-scale single pass sequencing of randomly picked cDNA clones, have been cost -effective and valuable resource for efficient and rapid identification of novel genes and development of molecular markers.…”

Section: Introductionmentioning

confidence: 99%

“…6,17 One can map ESTs to specific chromosome locations using physical mapping techniques, such as radiation hybrid mapping, happy mapping, or FISH. Alternatively, if the genome of the organism that originated the EST has been sequenced, one can align the EST sequence to that genome using a computer.…”

Section: Introductionmentioning

confidence: 99%

ESTs as a Resource for Gene Discovery and Population Genetic Analysis of Crop Plants

Ramesh¹

2017

MOJCSR

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In the advent of the genomic era, it has resulted in the vast production of publicly available DNA sequence data, including large collections of expressed sequence tags (ESTs) from a variety of different taxa. ESTs can be useful for gene identification, and with the involvement of in silico methodologies and the pathway-based analyses help to elucidate the biological functions and interactions of genes. ESTs encoding putative transcription factors (TFs) were identified by sequence comparison to known TF gene families of crop plants in the Plant Transcription Factor Database. Comparative mapping analysis of ESTs with other crops genome could reveal the phylogenetic relationships of several important genes. The utilization of these ESTs with computational studies will increase the understanding of genetic basis of the crop plants. Then the molecular markers based on ESTs such as EST-SSR, ESTSNPs providing the good source for the population genetics studies and useful for the marker-assisted breeding. These studies will make a great impact in crop improvement programs and keep the global food security. to EST based molecular markers significantly reveals the molecular base of a particular crop plant. Keywords

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Characterization of ESTs from black locust for gene discovery and marker development

Cited by 10 publications

References 30 publications

Integrated analysis of the physiology, RNA, and microRNA involved in black locust (Robinia pseudoacacia) rejuvenation

Integrated analysis of the physiology, RNA, and microRNA involved in black locust (Robinia pseudoacacia) rejuvenation

Development and Application of EST-SSR Markers for DNA Fingerprinting and Genetic Diversity Analysis of the Main Cultivars of Black Locust (Robinia pseudoacacia L.) in China

ESTs as a Resource for Gene Discovery and Population Genetic Analysis of Crop Plants

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