Genome-wide survey and expression analysis of F-box genes in chickpea

Gupta, Shefali; Garg, Vanika; Kant, Chandra; Bhatia, Sabhyata

doi:10.1186/s12864-015-1293-y

Cited by 77 publications

(62 citation statements)

References 68 publications

(124 reference statements)

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“…F-box proteins are involved in degradation of cellular proteins. F-box proteins can recognize a wide array of substrates and regulate many important biological processes such as embryogenesis, floral development, plant growth and development, biotic and abiotic stress, hormonal responses and senescence (Gupta et al 2015).…”

Section: Discussionmentioning

confidence: 99%

SSRmarker development from peanut gynophore transcriptome sequencing

et al. 2015

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Peanut is one of the most important oil crops in the world. To accelerate the marker‐assisted selection programmes of peanut, a transcriptome library of peanut gynophores at three different growth stages was constructed and sequenced using Illumina HiSeq™ 2000. Totally, 72 527 unigenes were assembled and mined for EST SSRs. A total of 5058 SSRs were obtained by using the SSR finding programme, which represented an average density of one SSR per 5.65 kb. Four thousand four hundred and forty‐two unigenes that contained one or more SSRs were identified. The most abundant SSRs in peanut are trinucleotides (55.1%) SSRs and followed by dinucleotides (33.2%). AG/CT (25.8%) repeats were the most abundant and followed by AAG/CTT (19.9%). Primers for 200 SSRs were designed for PCR amplification and for analysis of polymorphism in 22 peanut cultivars. Polymorphism could be detected by 17 SSRs among these cultivars. The newly developed SSR markers from peanut gynophore transcriptome sequencing will be an additional source of markers to the peanut community.

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Section: Discussionmentioning

confidence: 99%

SSRmarker development from peanut gynophore transcriptome sequencing

et al. 2015

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“…6). F-box domain recognizes a wide array of substrates and regulates many important biological processes by degrading cellular proteins in plants [37].…”

Section: Group-jmjd6mentioning

confidence: 99%

Systematic analysis of JmjC gene family of Brassica napus and KDM5 subfamily involved in abiotic stress response

Pan

Liu

et al. 2019

Preprint

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Background: Jumonji C (JmjC) proteins play an important role in plant development and stress response through the removal of lysine methylation from histones. Brassica napus, which originated from spontaneous hybridization between Brassica rapa and Brassica oleracea, is the most important oilseed crop after soybean, but evolutionary relationships and functions of JmjC proteins remain unclear. Results: 65 JmjC genes were identified from B. napus genome, 29 from B. rapa, and 23 from B. oleracea. These genes were grouped into seven clades according to conserved sequences, and their catalytic activities of demethylation were predicted. Group-KDM4/JHDM3 for H3K4/9/27/36, Group-KDM5A/B for H3K4, Group-JmjC domain-only A/B for H3K27/36, Group-KDM3/JHDM2 for H3K9, and Group-JMJD6 may be for arginine demethylases. B. napus inherited most of its JmjC genes from its parents. The average retention rate of B. napus JmjC gene from B. rapa (93.1%) and B. oleracea (82.6%) exceeded that of all homologous gene pairs (83.7%) across the whole B. napus genome. Thirteen new or duplicated JmjC genes have emerged in B. napus. Sequence similarity and domain organization analyses suggest that the functions of these genes might be diversified. Furthermore, KDM5 genes were examined under stress conditions due to H3K4 demethylation. Expression profiles indicated that the genes from B. napus are possibly involved in various stress responses. Conclusion: This study provides the first genome-wide characterization of JmjC genes in Brassica species. Its JmjC genes potentially have diverse functions, and its KDM5 genes might be involved in stress response. The results of this study facilitate the future functional characterization of the demethylation of JmjC family in Brassica crops.

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“…It was identified that model plants of Arabidopsis contain 694 F-box genes [23]. Important crops also contain F-box genes-for example, rice, maize, soybean, and chickpea contain 678, 509, 359, and 285 F-box genes, respectively [25][26][27][28]. The same applies to perennial fruit crops, such as apples and pears, which contain 517 and 226 F-box genes, respectively [24,29], as well as perennial woody plants, such as Populus trichocarpa Torr.…”

Section: Introductionmentioning

confidence: 99%

“…The number of F-box genes of woody plants and herbaceous annual plants (Arabidopsis thaliana (L.) Heynh., rice, maize, and soybean) has high variation [24][25][26][27]29,30]. Under abiotic stresses, the expression profiles showed that the F-box gene family members play a crucial role in stress responsive pathways [25,28,31]. A total of 972 F-box genes were found in Medicago (Medicago truncatula Gaertn.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Transcriptional Expression Profiles of the F-box Gene Family in Common Walnut (Juglans regia L.)

Yan

Zhou

Yue

et al. 2019

Forests

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The common walnut (or Persian walnut), Juglans regia L., is an economically important temperate tree species valued for both its edible nut and high-quality wood. F-box gene family members are involved in plant development, which includes regulating plant development, reproduction, cellular protein degradation, response to biotic and abiotic stresses, and flowering. However, in common walnut (J. regia), there are no reports about the F-box gene family. Here, we report a genome-wide identification of J. regia F-box genes and analyze their phylogeny, duplication, microRNA, pathway, and transcriptional expression profile. In this study, 74 F-box genes were identified and clustered into three groups based on phylogenetic analysis and eight subfamilies based on special domains in common walnut. These common walnut F-box genes are distributed on 31 different pseudo-chromosomes. The gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and microRNA profiles showed that the F-box gene family might play a critical role in the flowering of common walnut. The expressions were significantly higher in female flowers and male flowers compared with leaf and hull tissues at a transcriptome level. The results revealed that the expressions of the F-box gene in female flowers were positively correlated with male flowers, but there was no correlation between any other tissue combinations in common walnut. Our results provided insight into the general characteristics of the F-box genes in common walnut.

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Genome-wide survey and expression analysis of F-box genes in chickpea

Cited by 77 publications

References 68 publications

SSRmarker development from peanut gynophore transcriptome sequencing

SSRmarker development from peanut gynophore transcriptome sequencing

Systematic analysis of JmjC gene family of Brassica napus and KDM5 subfamily involved in abiotic stress response

Genome-Wide Identification and Transcriptional Expression Profiles of the F-box Gene Family in Common Walnut (Juglans regia L.)

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