Resources for studies of iron walnut (Juglans sigillata) gene expression, genetic diversity, and evolution

Feng, Xiaojia; Xu, Yuan; Sun, Yiwei; Hu, Yiheng; Zulfiqar, Saman; Ouyang, Xianheng; Dang, Meng; Zhou, Huijuan; Woeste, Keith; Zhao, Peng

doi:10.1007/s11295-018-1263-z

Cited by 14 publications

(8 citation statements)

References 49 publications

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“…The resulting measurements found that most genes in the family Acanthaceae were under negative selection (ω <1) except for ycf15 (ω = 1.4453). According to previous studies, the ycf15 gene is a member of the PFAM protein family accession PF10705 (Sara et al, 2018) and was not considered to be a protein-coding gene because of its unknown function (Steane, 2005;Feng et al, 2018). The ycf15 gene acts as a pseudogene in some species because of its premature stop codons (Chen et al, 2018;Jiang et al, 2018).…”

Section: Adaptive Evolution Analysismentioning

confidence: 99%

Comparative analysis of chloroplast genomes for fiveDiclipteraspecies (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution

Huang

Cano

et al. 2020

PeerJ

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The genus Dicliptera (Justicieae, Acanthaceae) consists of approximately 150 species distributed throughout the tropical and subtropical regions of the world. Newly obtained chloroplast genomes (cp genomes) are reported for five species of Dilciptera (D. acuminata, D. peruviana, D. montana, D. ruiziana and D. mucronata) in this study. These cp genomes have circular structures of 150,689–150,811 bp and exhibit quadripartite organizations made up of a large single copy region (LSC, 82,796–82,919 bp), a small single copy region (SSC, 17,084–17,092 bp), and a pair of inverted repeat regions (IRs, 25,401–25,408 bp). Guanine-Cytosine (GC) content makes up 37.9%–38.0% of the total content. The complete cp genomes contain 114 unique genes, including 80 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Comparative analyses of nucleotide variability (Pi) reveal the five most variable regions (trnY-GUA-trnE-UUC, trnG-GCC, psbZ-trnG-GCC, petN-psbM, and rps4-trnL-UUA), which may be used as molecular markers in future taxonomic identification and phylogenetic analyses of Dicliptera. A total of 55-58 simple sequence repeats (SSRs) and 229 long repeats were identified in the cp genomes of the five Dicliptera species. Phylogenetic analysis identified a close relationship between D. ruiziana and D. montana, followed by D. acuminata, D. peruviana, and D. mucronata. Evolutionary analysis of orthologous protein-coding genes within the family Acanthaceae revealed only one gene, ycf15, to be under positive selection, which may contribute to future studies of its adaptive evolution. The completed genomes are useful for future research on species identification, phylogenetic relationships, and the adaptive evolution of the Dicliptera species.

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Section: Adaptive Evolution Analysismentioning

confidence: 99%

Comparative analysis of chloroplast genomes for fiveDiclipteraspecies (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution

Huang

Cano

et al. 2020

PeerJ

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“…The resulting measurements found that most genes in the family Acanthaceae were under negative selection (ω <1) except for ycf15 (ω =1.4453). According to previous studies, the ycf15 gene is a member of the PFAM protein family accession PF10705 (Sara et al, 2019) and was not considered to be a protein-coding gene because of its unknown function (Steane, 2005;Feng et al, 2018). The ycf15 gene acts as a pseudogene in some species because of its premature stop codons (Chen et al, 2018;Jiang et al, 2018).…”

Section: Adaptive Evolution Analysismentioning

confidence: 99%

Peer Review #2 of "Comparative analysis of chloroplast genomes for five Dicliptera species (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution (v0.1)"

Khan¹

2020

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The genus Dicliptera (Justicieae, Acanthaceae) consists of approximately 150 species distributed throughout the tropical and subtropical regions of the world. Newly obtained chloroplast genomes (cp genomes) are reported for five species of Dilciptera (D. acuminata, D. peruviana, D. montana, D. ruiziana and D. mucronata) in this study. These cp genomes have circular structures of 150689-150811 bp and exhibit quadripartite organizations made up of a large single copy region (LSC, 82796-82919 bp), a small single copy region (SSC, 17084-17092 bp), and a pair of inverted repeat regions (IRs, 25401-25408 bp). Guanine-Cytosine (GC) content makes up 37.9%-38.0% of the total content. The complete cp genomes contain 114 unique genes, including 80 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Comparative analyses of nucleotide variability (Pi) reveal the 5 most variable regions (trnY-GUA-trnE-UUC, trnG-GCC, psbZ-trnG-GCC, petN-psbM, and rps4-trnL-UUA), which may be used as molecular markers in future taxonomic identification and phylogenetic analyses of Dicliptera. A total of 55-58 simple sequence repeats (SSRs) and 229 long repeats were identified in the cp genomes of the five Dicliptera species. Phylogenetic analysis identified a close relationship between D. ruiziana and D. montana, followed by D. acuminata, D. peruviana, and D. mucronata. Evolutionary analysis of orthologous protein-coding genes within the family Acanthaceae revealed only one gene, ycf15, to be under positive selection, which may contribute to future studies of its adaptive evolution. The completed genomes are useful for future research on species identification, phylogenetic relationships, and the adaptive evolution of the Dicliptera species.

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“…Alleles SFB1, SFB2, SFB4, and SFB5 in sweet cherry proved to play a self-incompatible effect by affecting the development of pollen tubes. Allele S4sm, lacking the SFBB1-S4 protein, caused no significant effect on pollen tubes, while the S5 haplotype encoding the SFBB1 protein could cause pistils to accept other genes [29,[35][36][37][38][39][40]; thus, there is strong evidence that the F-box gene is relevant in pollen development. In this study, the results showed that some genes (Jure 07950.t1, Jure 21178.t1, Jure 11456.t1, Jure 07156.t1, Jure 07788.t1, Jure 21675.t1, Jure 19792.t1, Jure 05249.t1, Jure 26563.t1, Jure 20019.t1, Jure 14341.t1, and Jure 26807.t1) were expressed highly in female flowers, suggesting that the F-box gene family of common walnut was vital for regulating the flowering (Figures 4-6).…”

Section: Function Of the F-box Genesmentioning

confidence: 99%

“…Walnuts and butternuts (Juglans) are known for their edible nuts and high-quality wood [38,39]. It is an ecologically important tree species valued for both its nuts and wood since ancient times [39,40]. J. regia is diploid monoecious and heterodichogamous.…”

Section: Introductionmentioning

confidence: 99%

“…J. regia is diploid monoecious and heterodichogamous. It is wind-pollinated and highly heterozygous [40]. There is no previous study regarding the F-box gene in common walnut; comprehensive information and functional characterization of the F-box gene family of common walnut (J. regia) is still unclear, especially the expression profiles in male and female flowers.…”

Section: Introductionmentioning

confidence: 99%

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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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Resources for studies of iron walnut (Juglans sigillata) gene expression, genetic diversity, and evolution

Cited by 14 publications

References 49 publications

Comparative analysis of chloroplast genomes for fiveDiclipteraspecies (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution

Comparative analysis of chloroplast genomes for fiveDiclipteraspecies (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution

Peer Review #2 of "Comparative analysis of chloroplast genomes for five Dicliptera species (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution (v0.1)"

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

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