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Genome-Wide Identification and Comparative Analysis of ARF Family Genes in Three Apiaceae Species

Pei, Qiaoying, Li, Nan, Yang, Qihang, Wu, Tong, Feng, Shuyan, Feng, Xuehuan, Jing, Zange, Zhou, Rong, Gong, Ke, Yu, Tong, Wang, Zhen, Song, Xiaoming·2021·Frontiers in Genetics
DOI 10.3389/fgene.2020.590535PMC PMC7838617
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Abstract

The family Apiaceae includes many important vegetables and medicinal plants. Auxin response factors (ARFs) play critical roles in regulating plant growth and development. Here, we performed a comprehensive analysis of the ARF gene family in three Apiaceae species, celery, coriander, and carrot, and compared the results with the ARF gene family of lettuce, Arabidopsis, and grape. We identified 156 ARF genes in all six species and 89 genes in the three Apiaceae species, including 28, 34, and 27 in celery, coriander, and carrot, respectively. The paralogous gene number in coriander was far greater than that in carrot and celery. Our analysis revealed that ARF genes of the three Apiaceae species in 34 branches of the phylogenetic tree underwent significant positive selection. Additionally, our findings indicated that whole-genome duplication played an important role in ARF gene family expansion. Coriander contained a greater number of ARF genes than celery and carrot because of more gene duplications and less gene losses. We also analyzed the expression of ARF genes in three tissues by RNA-seq and verified the results by quantitative real-time PCR. Furthermore, we found that several paralogous genes exhibited divergent expression patterns. Overall, this study provides a valuable resource for exploring how ARF family genes regulate plant growth and development in other plants. Since this is the first report of the ARF gene family in Apiaceae, our results will serve as a guide for comparative and functional analyses of ARF and other gene families in Apiaceae.

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FIGURE 1 Phylogenetic analysis of ARF amino acid sequences in three Apiaceae species (carrot, celery, and coriander), lettuce, grape, and Arabidopsis. The phylogenetic tree was generated using the IQ-TREE software with the maximum likelihood (ML) based on the JTT + F + R8 model and 1,000 bootstrap replications.
FIGURE 1 Phylogenetic analysis of ARF amino acid sequences in three Apiaceae species (carrot, celery, and coriander), lettuce, grape, and Arabidopsis. The phylogenetic tree was generated using the IQ-TREE software with the maximum likelihood (ML) based on the JTT + F + R8 model and 1,000 bootstrap replications.CC BY · PubMed Central
FIGURE 2 Analysis of paralogous and orthologous ARF gene pairs. (A) Circos plot of ARF gene paralogs and orthologs in three Apiaceae species. (B) Ks and Ka/Ks values of orthologous ARF gene pairs between any two of three Apiaceae species. (C) Divergence time of orthologous ARF gene pairs between any two of three Apiaceae species.
FIGURE 2 Analysis of paralogous and orthologous ARF gene pairs. (A) Circos plot of ARF gene paralogs and orthologs in three Apiaceae species. (B) Ks and Ka/Ks values of orthologous ARF gene pairs between any two of three Apiaceae species. (C) Divergence time of orthologous ARF gene pairs between any two of three Apiaceae species.CC BY · PubMed Central
FIGURE 3 Duplication, loss, and positive selection analysis of ARF genes in three Apiaceae species. (A) Percentage of different duplication types for ARF genes and all other genes. (B) Analysis of ARF gene duplication and loss. The “ + ” and “–” symbols indicate ARF gene duplication and loss, respectively, and the values after these symbols represent gene number. (C) Positive selection of ARF genes in celery, coriander, and carrot. Red stars represent positive selection branches.
FIGURE 3 Duplication, loss, and positive selection analysis of ARF genes in three Apiaceae species. (A) Percentage of different duplication types for ARF genes and all other genes. (B) Analysis of ARF gene duplication and loss. The “ + ” and “–” symbols indicate ARF gene duplication and loss, respectively, and the values after these symbols represent gene number. (C) Positive selection of ARF genes in celery, coriander, and carrot. Red stars represent positive selection branches.CC BY · PubMed Central
FIGURE 4 Relative expression level (FPKM) of celery ARF paralogous gene pairs in the root, petiole, and leaf. Asterisks indicate significant differences (*P < 0.05, **P < 0.01).
FIGURE 4 Relative expression level (FPKM) of celery ARF paralogous gene pairs in the root, petiole, and leaf. Asterisks indicate significant differences (*P < 0.05, **P < 0.01).CC BY · PubMed Central

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Cited by

Metadata

Authors
Pei, Q., Li, N., Yang, Q., Wu, T., Feng, S., Feng, X., Jing, Z., Zhou, R., Gong, K., Yu, T., Wang, Z., & Song, X.
Venue
Frontiers in Genetics
Publisher
Frontiers Media SA
Published
2021-01-13
Volume
11
ISSN
1664-8021
DOI
10.3389/fgene.2020.590535
PMC
PMC7838617
Cited by
18
References
0
Licence
creativecommons.org/licenses/by/4.0/ (vor)

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