杜仲ARF基因家族全基因组鉴定和表达分析

doi:10.11707/j.1001-7488.20210318

Abstract

Abstract:

Objective: Eucommia ulmoides is a traditional medicinal and rubber woody plant that is endemic to China. It is important to study the genes related to growth and development for breeding. Auxin response factor(ARF) is an important transcription factor in the auxin signaling pathways. Study of the role of ARF in E. ulmoides organ development has great values both in theory and practice. Method: Identification of putative EuARF genes from genome data and bio-informatics analysis were performed. The phylogenetic tree was generated using a multiple sequence alignment of the EuARF, AtARF (Arabidopsis thaliana ARF), OsARF (Oryza sativa ARF) and PeARF (Populus×euramericana ARF) proteins. RNA-seq data were used to analyze EuARFs expression profiles. qRT-PCR were used to analyze the expression patterns of these genes and miRNAs in organs at different developmental stages. Result: A total of 18 EuARFs were identified in the E. ulmoides genome. These EuARFs were divided into five classes by phylogenetic tree and predicted that eu-miR160s target EuARFs of class Ⅱ and eu-miR167s target EuARFs of class Ⅴ except EuARF8.2. The expression patterns showed that the expression of EuARFs in different growth stages of leaves was different, and the expression of EuARFs in class Ⅴ and EuARF19.2 in class Ⅵ were higher in 3 cm long growing leaves and unfolded young leaves. The qRT-PCR indicated that EuARFs expressed in organs (leaf, root and stem) at different developmental stages (young and mature). In addition, EuARFs were up-regulated in mature roots and down-regulated in mature leaves and stems. Meanwhile eu-miR160s was mainly expressed in young roots, and eu-miR167s was mainly expressed in mature leaves. Conclusion: A total of 18 EuARFs were identified in the genome of E. ulmoides. These EuARFs were expressed in organs (roots, stems and leaves) at different developmental stages (young and mature) under normal growth conditions. The expression level indicates that EuARFs in class V has a regulating role for seedlings growth and development and EuARF19.2 plays an important role in regulating the leaf growth.

Key words: Eucommia ulmoides, auxin response factor, gene expression patterns, miRNA regulation

CLC Number:

S718.46

Minhao Liu,Long Li,Jing Ye,Xuanyuan Zhou,Zhouqi Li,Ruishen Fan,Junlei Xu. Genome-Wide Identification and Expression Analysis of the ARF Gene Family in Eucommia ulmoides[J]. Scientia Silvae Sinicae, 2021, 57(3): 170-180.

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miRNA	序列Sequences (5′—3′)	茎环引物Stem ring primer (5′—3′)	正向引物Forward primer (5′—3′)
eu-miR160d	TGCCTGGCTCCCTGCATGCCA	CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGCTGGCATGC	TCGGCAGGTGCCTGGCTCCCT
eu-miR160f	TGCCTGGCTCCCTGTATGCC	CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGCGGCATACA	TCGGCAGGTGCCTGGCTCCC
eu-miR167a	TGAAGCTGCCAGCATGATCTC	CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGCGAGATCAT	TCGGCAGGTGAAGCTGCCAGC
eu-miR167d	TGAAGCTGCCAGCATGATCT	CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGCAGATCATG	TCGGCAGGTGAAGCTGCCAG

基因 Gene	正向引物Forward primer (5′—3′)	反向引物Reverse primer (5′—3′)
EuARF1	CTTCAGGTGCCAAGCCTAGTTCTC	GCCGGTCTTCTTATGCCAGTGTC
EuARF2.1	CCATAGTGAACAGGTGGCAGCATC	GGTTGGAGCGTCATCTGAGCATAC
EuARF2.2	GCATGGCATACTTGCGAGTG	CCGAACGAGTAATCATATTCAACAG
EuARF3.1	ACGAAGGTGACATGATGCTGATGG	TCGTTGCCGCTGCCAATTCC
EuARF3.2	AGCCAGCACCATCACTTCC	AGCCAGCACCATCACTTCC
EuARF4	GAAGGTTCAGCGGTCTTGTG	TCCCATTTCACTATCAAGCATCTC
EuARF6.1	TCGCCACAAGAGGTGCAGGAG	GCATGGTCATCGCAGCTACTATCG
EuARF6.2	GATACTATCGCCGCTGGAAGTGC	TGTCGCCGTTGCCGTGATTAAG
EuARF8.1	CATTGGAGATCCGTCAAGGTTGGTT	ATGGGAAAGGTTGTCAAAGGCTCAA
EuARF8.2	GGGCTTGTCCATCTGAGTTTG	GCACCAGTTTGACGACCTTC
EuARF9	TCCACAGCAACAGATGACACAACC	GCTGCGGAAGCTGAGAGTATAACG
EuARF10.1	GCGTCCTGGGATGAGGTTTA	CTGAAGACACTGCCATGAAGAAT
EuARF10.2	TTGGAACAGACGATACAGCAGACAA	GAGCCAGGCCATCTAGCAGGAT
EuARF16	TCGTCAACCGCAAGAAGCTCATC	GCGTTGGCTGAAGGTAGAGGAAG
EuARF17	ATGTGAAGCGTGTCAGCCCTTG	AGGTGGTGAGAACTGTGGAATCTGA
EuARF18	ACCGACAGCGAGAATGACATGATG	GCCGACAGATGAAGACTTGGACAG
EuARF19.1	GGTGCGGTGGGATGAAACTTCTAC	CAGGAGTCAGGGCAGGCTCTATT
EuARF19.2	TTGCCTCAGGTTGGAAGTCTTGTC	GTCTGCGTGTAATGTGGCGTTATG

基因 Gene	基因编号 Gene ID	蛋白长度 Protein length (aa)	等电点 pI	分子量 Molecular weight/ kDa	结构域 Domain
EuARF1	GWHGAAAL013439	668	6.15	74.75	DBD, MR, CTD
EuARF2.1	GWHGAAAL012635	822	7.62	91.97	DBD, MR, CTD
EuARF2.2	GWHGAAAL023550	577	6.18	65.12	DBD, MR, CTD
EuARF3.1	GWHGAAAL026509	638	6.27	70.13	DBD, ARF
EuARF3.2	GWHGAAAL025681	823	6.69	90.37	DBD, ARF
EuARF4	GWHGAAAL008814	846	5.91	94.44	DBD, MR, CTD
EuARF6.1	GWHGAAAL000541	892	5.75	99.40	DBD, MR, CTD
EuARF6.2	GWHGAAAL008938	858	5.76	95.04	DBD, MR, CTD
EuARF8.1	GWHGAAAL000541	892	5.75	99.40	DBD, MR, CTD
EuARF8.2	GWHGAAAL000012	273	9.68	30.64	DBD, ARF
EuARF9	GWHGAAAL016769	653	5.68	73.19	DBD, MR, CTD
EuARF10.1	GWHGAAAL008845	631	6.19	69.97	DBD, ARF
EuARF10.2	GWHGAAAL008846	633	5.36	70.70	DBD, ARF
EuARF16	GWHGAAAL011358	682	6.96	74.95	DBD, ARF
EuARF17	GWHGAAAL001628	526	5.63	57.54	DBD, ARF
EuARF18	GWHGAAAL025932	623	6.04	70.23	DBD, MR, CTD
EuARF19.1	GWHGAAAL003011	1 062	6.05	117.84	DBD, MR, CTD
EuARF19.2	GWHGAAAL003601	1 013	6.12	111.39	DBD, MR, CTD

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Genome-Wide Identification and Expression Analysis of the ARF Gene Family in Eucommia ulmoides

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