Genome-wide identification and characterization of laccase gene family in Citrus sinensis

Xu, Xiaogang; Zhou, Yipeng; Wang, Bin; Ding, Li; Wang, Yue; Luo, Li; Zhang, Yueliang; Kong, Weiwen

doi:10.1016/j.gene.2018.12.015

Cited by 43 publications

(47 citation statements)

References 39 publications

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“…Adding SmLACs to the tree resulted in separation of AtLAC6 and PtLAC33 from C6. Similar results were observed in a tree constructed for AtLACs and Citrus sinensis CsLACs (Xu et al, 2019). This suggests that the relationships between C6 and C7 members are indeed relatively far.…”

Section: Discussionsupporting

confidence: 84%

Analysis of the laccase gene family and miR397-/miR408-mediated posttranscriptional regulation in Salvia miltiorrhiza

Li¹,

Li²,

Zhou³

et al. 2019

PeerJ

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Salvia miltiorrhiza is one of the most commonly used traditional Chinese medicine materials. It contains important bioactive phenolic compounds, such as salvianolic acids, flavonoids and anthocyanins. Elucidation of phenolic compound biosynthesis and its regulatory mechanism is of great significance for S. miltiorrhiza quality improvement. Laccases (LACs) are multicopper-containing enzymes potentially involved in the polymerization of phenolic compounds. So far, little has been known about LAC genes in S. miltiorrhiza. Through systematic investigation of the whole genome sequence and transcriptomes of S. miltiorrhiza, we identified 65 full-length SmLAC genes (SmLAC1–SmLAC65). Phylogenetic analysis showed that 62 of the identified SmLACs clustered with LACs from Arabidopsis and Populus trichocarpa in seven clades (C1–C7), whereas the other three fell into one S. miltiorrhiza-specific clade (C8). All of the deduced SmLAC proteins contain four conserved signature sequences and three typical Cu-oxidase domains, and gene structures of most LACs from S. miltiorrhiza, Arabidopsis and P. trichocarpa were highly conserved, however SmLACs encoding C8 proteins showed distinct intron-exon structures. It suggests the conservation and diversity of plant LACs in gene structures. The majority of SmLACs exhibited tissue-specific expression patterns, indicates manifold functions of SmLACs played in S. miltiorrhiza. Analysis of high-throughput small RNA sequences and degradome data and experimental validation using the 5′ RACE method showed that 23 SmLACs were targets of Smi-miR397. Among them, three were also targeted by Smi-miR408. It suggests the significance of miR397 and miR408 in posttranscriptional regulation of SmLAC genes. Our results provide a foundation for further demonstrating the functions of SmLACs in the production of bioactive phenolic compounds in S. miltiorrhiza.

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Section: Discussionsupporting

confidence: 84%

Analysis of the laccase gene family and miR397-/miR408-mediated posttranscriptional regulation in Salvia miltiorrhiza

Li¹,

Li²,

Zhou³

et al. 2019

PeerJ

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“…This indicates that the laccase genes not only vary between different species, but also between different varieties. Signal peptide sequence deficiency was also reported in Flammulina velutipes and Setosphaeria turcica [32,33], as well as in plants [34], implying that the laccase gene may have lost the signal peptide sequence during evolution.…”

Section: Discussionmentioning

confidence: 90%

Expression Profile of Laccase Gene Family in White-Rot Basidiomycete Lentinula edodes under Different Environmental Stresses

Yan

Bian

et al. 2019

Genes

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Laccases belong to ligninolytic enzymes and play important roles in various biological processes of filamentous fungi, including fruiting-body formation and lignin degradation. The process of fruiting-body development in Lentinula edodes is complex and is greatly affected by environmental conditions. In this paper, 14 multicopper oxidase-encoding (laccase) genes were analyzed in the draft genome sequence of L. edodes strain W1-26, followed by a search of multiple stress-related Cis-elements in the promoter region of these laccase genes, and then a transcription profile analysis of 14 laccase genes (Lelcc) under the conditions of different carbon sources, temperatures, and photoperiods. All laccase genes were significantly regulated by varying carbon source materials. The expression of only two laccase genes (Lelcc5 and Lelcc6) was induced by sodium-lignosulphonate and the expression of most laccase genes was specifically upregulated in glucose medium. Under different temperature conditions, the expression levels of most laccase genes decreased at 39 °C and transcription was significantly increased for Lelcc1, Lelcc4, Lelcc5, Lelcc9, Lelcc12, Lelcc13, and Lelcc14 after induction for 24 h at 10 °C, indicating their involvement in primordium differentiation. Tyrosinase, which is involved in melanin synthesis, was clustered with the same group as Lelcc4 and Lelcc7 in all the different photoperiod treatments. Meanwhile, five laccase genes (Lelcc8, Lelcc9, Lelcc12, Lelcc13, and Lelcc14) showed similar expression profiles to that of two blue light receptor genes (LephrA and LephrB) in the 12 h light/12 h dark treatment, suggesting the involvement of laccase genes in the adaptation process of L. edodes to the changing environment and fruiting-body formation. This study contributes to our understanding of the function of the different Lelcc genes and facilitates the screening of key genes from the laccase gene family for further functional research.

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“…1 ), rice and barley ( Hordeum vulgare ) [ 36 , 37 ]. Gene clustering has also been observed in many other gene families, such as the LEA gene family in B. napus [ 38 ] and Phyllostachys edulis [ 39 ] and laccase gene family in Citrus sinensis [ 40 ]. The LEA gene clusters on B. napus chromosomes A9 and C4 probably resulted from chromosomal rearrangement during the evolution of Brassica species [ 38 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification of the restorer-of-fertility-like (RFL) gene family in Brassica napus and expression analysis in Shaan2A cytoplasmic male sterility

Ning

Wang

et al. 2020

BMC Genomics

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Background Cytoplasmic male sterility (CMS) is very important in hybrid breeding. The restorer-of-fertility (Rf) nuclear genes rescue the sterile phenotype. Most of the Rf genes encode pentatricopeptide repeat (PPR) proteins. Results We investigated the restorer-of-fertility-like (RFL) gene family in Brassica napus. A total of 53 BnRFL genes were identified. While most of the BnRFL genes were distributed on 10 of the 19 chromosomes, gene clusters were identified on chromosomes A9 and C8. The number of PPR motifs in the BnRFL proteins varied from 2 to 19, and the majority of BnRFL proteins harbored more than 10 PPR motifs. An interaction network analysis was performed to predict the interacting partners of RFL proteins. Tissue-specific expression and RNA-seq analyses between the restorer line KC01 and the sterile line Shaan2A indicated that BnRFL1, BnRFL5, BnRFL6, BnRFL8, BnRFL11, BnRFL13 and BnRFL42 located in gene clusters on chromosomes A9 and C8 were highly expressed in KC01. Conclusions In the present study, identification and gene expression analysis of RFL gene family in the CMS system were conducted, and seven BnRFL genes were identified as candidates for the restorer genes in Shaan2A CMS. Taken together, this method might provide new insight into the study of Rf genes in other CMS systems.

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Genome-wide identification and characterization of laccase gene family in Citrus sinensis

Cited by 43 publications

References 39 publications

Analysis of the laccase gene family and miR397-/miR408-mediated posttranscriptional regulation in Salvia miltiorrhiza

Analysis of the laccase gene family and miR397-/miR408-mediated posttranscriptional regulation in Salvia miltiorrhiza

Expression Profile of Laccase Gene Family in White-Rot Basidiomycete Lentinula edodes under Different Environmental Stresses

Genome-wide identification of the restorer-of-fertility-like (RFL) gene family in Brassica napus and expression analysis in Shaan2A cytoplasmic male sterility

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