Biotechnology Bulletin ›› 2021, Vol. 37 ›› Issue (4): 18-27.doi: 10.13560/j.cnki.biotech.bull.1985.2020-1128
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GAO Ling(), WANG Fei, XIE Shuang-quan, CHEN Xi-feng, SHEN Hai-tao, LI Hong-bin()
Received:
2020-09-05
Online:
2021-04-26
Published:
2021-05-13
Contact:
LI Hong-bin
E-mail:1425446422@qq.com;lihb@shzu.edu.cn
GAO Ling, WANG Fei, XIE Shuang-quan, CHEN Xi-feng, SHEN Hai-tao, LI Hong-bin. Genome-wide Identification and Expression Analysis of CBL Gene Family in Glycyrrhiza uralensis[J]. Biotechnology Bulletin, 2021, 37(4): 18-27.
引物名称Primer name | 引物序列Primer sequence(5'-3') | 引物功能 Primer function |
---|---|---|
GuCBL1-F | CGAGCTTGACGTTGGGAGAG | GuCBL的RT-PCR检测 qRT-PCR detection of GuCBL |
GuCBL1-R | CTGGCGAGGGCGACAATATC | |
GuCBL2-F | TTTGTTTGCTGATCGGGTGT | |
GuCBL2-R | ATTCCGCAAGCGTAGCAACT | |
GuCBL3-F | CCGATTCGTCAAAGCAACCT | |
GuCBL3-R | AGGATCCCATTGTGCTTTGTG | |
GuCBL4-F | GAGAGGCGGTTTGCGTATTG | |
GuCBL4-R | GCCTTTTTACGGTTCCTGGC | |
GuCBL5-F | TGTCAGTGAGGTTGAGGCATT | |
GuCBL5-R | CGCATTTGGGTGGAAGACAT | |
GuCBL6-F | GCAGTGCAGTTATTGACGATGG | |
GuCBL6-R | TGATGCACTGGGATGGAAGAC | |
GuCBL7-F | GCTGTGTGCGGTGTTCATTC | |
GuCBL7-R | GCGCAACGCCTCAATTTCAT | |
GuCBL8-F | ATGAGGATCCCACCGTTCTTG | |
GuCBL8-R | ACCCCATTGCGCTTGACATC | |
GuCBL9-F | TCCTTGCTTCTGAAACACCCT | |
GuCBL9-R | TGGCCATTGCGATTGACATC | |
GuCBL10-F | CAGCAACAGCACAGGCATTT | |
GuCBL10-R | CAGCAAGGCGAGCGAAATC | |
GuActin-F | CCTCAACCCAAAGGTCAACAG | 内参基因 Internal reference gene |
GuActin-R | GACCAGCGAGATCCAAACGAA | |
GuCBL4-1 | GAAATTGAAGCATTATATGATCTGT | 全长基因克隆 Full-length gene cloning |
GuCBL4-2 | GGAGCCTATGGAAAAACGCCAGCAA | |
GuCBL7-1 | ACTTCGTAGCTAGCACTCCG | |
GuCBL7-2 | GACTGCATGATGGCGGAAAA | |
GuCBL10-1 | AGCAACAGCACAGGCATTTCC | |
GuCBL10-2 | CAGCCTCCGATTTGAAAACAAAACT |
Table 1 Primers used in this study
引物名称Primer name | 引物序列Primer sequence(5'-3') | 引物功能 Primer function |
---|---|---|
GuCBL1-F | CGAGCTTGACGTTGGGAGAG | GuCBL的RT-PCR检测 qRT-PCR detection of GuCBL |
GuCBL1-R | CTGGCGAGGGCGACAATATC | |
GuCBL2-F | TTTGTTTGCTGATCGGGTGT | |
GuCBL2-R | ATTCCGCAAGCGTAGCAACT | |
GuCBL3-F | CCGATTCGTCAAAGCAACCT | |
GuCBL3-R | AGGATCCCATTGTGCTTTGTG | |
GuCBL4-F | GAGAGGCGGTTTGCGTATTG | |
GuCBL4-R | GCCTTTTTACGGTTCCTGGC | |
GuCBL5-F | TGTCAGTGAGGTTGAGGCATT | |
GuCBL5-R | CGCATTTGGGTGGAAGACAT | |
GuCBL6-F | GCAGTGCAGTTATTGACGATGG | |
GuCBL6-R | TGATGCACTGGGATGGAAGAC | |
GuCBL7-F | GCTGTGTGCGGTGTTCATTC | |
GuCBL7-R | GCGCAACGCCTCAATTTCAT | |
GuCBL8-F | ATGAGGATCCCACCGTTCTTG | |
GuCBL8-R | ACCCCATTGCGCTTGACATC | |
GuCBL9-F | TCCTTGCTTCTGAAACACCCT | |
GuCBL9-R | TGGCCATTGCGATTGACATC | |
GuCBL10-F | CAGCAACAGCACAGGCATTT | |
GuCBL10-R | CAGCAAGGCGAGCGAAATC | |
GuActin-F | CCTCAACCCAAAGGTCAACAG | 内参基因 Internal reference gene |
GuActin-R | GACCAGCGAGATCCAAACGAA | |
GuCBL4-1 | GAAATTGAAGCATTATATGATCTGT | 全长基因克隆 Full-length gene cloning |
GuCBL4-2 | GGAGCCTATGGAAAAACGCCAGCAA | |
GuCBL7-1 | ACTTCGTAGCTAGCACTCCG | |
GuCBL7-2 | GACTGCATGATGGCGGAAAA | |
GuCBL10-1 | AGCAACAGCACAGGCATTTCC | |
GuCBL10-2 | CAGCCTCCGATTTGAAAACAAAACT |
基因名称 Gene name | 染色体位置 Chromosome location | 开放阅读框长度 Open reading frame sequence length/bp | 氨基酸数目Amino acid number/aa | 分子量Molecular weight/kD | 等电点Isoelectric point | N-端氨基酸 N-terminal amino acid | 棕榈酰化位点 Palmitoylation site | 豆蔻酰化位点 Myristoylation site | 亚细胞定位 Subcellular localization |
---|---|---|---|---|---|---|---|---|---|
GuCBL1 | Scaffold00021(+):357697-361866 | 828 | 275 | 31.68 | 4.99 | MMIDMDFS | √ | × | 质膜 Plasma membrane |
GuCBL2 | Scaffold00027(+):170105-174365 | 699 | 232 | 26.76 | 4.77 | MVKRDIML | √ | × | 质膜 Plasma membrane |
GuCBL3 | Scaffold00030(-):499662-505101 | 750 | 249 | 28.71 | 4.93 | MPDSDSLF | √ | × | 质膜 Plasma membrane |
GuCBL4 | Scaffold00036(-):366361-373219 | 1 008 | 331 | 37.63 | 9.31 | WLIFQKLK | √ | × | 质膜 Plasma membrane |
GuCBL5 | Scaffold00067(+):227402-231449 | 642 | 213 | 24.36 | 4.67 | MGCFNSKA | √ | √ | 质膜 Plasma membrane |
GuCBL6 | Scaffold00088(-):140793-143426 | 681 | 226 | 25.72 | 4.57 | MVQFLDEL | √ | × | 质膜 Plasma membrane |
GuCBL7 | Scaffold00219(-):429-5651 | 861 | 364 | 41.46 | 5.33 | MDFVASTP | √ | × | 质膜 Plasma membrane |
GuCBL8 | Scaffold00461(-):93781-104251 | 651 | 216 | 24.87 | 4.76 | MGCYCSTS | √ | √ | 质膜 Plasma membrane |
GuCBL9 | Scaffold00669(-):36499-39615 | 717 | 238 | 27.41 | 5.38 | MGCRSSKV | √ | √ | 质膜 Plasma membrane |
GuCBL10 | Scaffold01818(+):19453-23753 | 735 | 269 | 31.13 | 5.35 | MLQQQHRH | √ | × | 质膜 Plasma membrane |
Table 2 Characteristic analysis of G. uralensis CBL family genes
基因名称 Gene name | 染色体位置 Chromosome location | 开放阅读框长度 Open reading frame sequence length/bp | 氨基酸数目Amino acid number/aa | 分子量Molecular weight/kD | 等电点Isoelectric point | N-端氨基酸 N-terminal amino acid | 棕榈酰化位点 Palmitoylation site | 豆蔻酰化位点 Myristoylation site | 亚细胞定位 Subcellular localization |
---|---|---|---|---|---|---|---|---|---|
GuCBL1 | Scaffold00021(+):357697-361866 | 828 | 275 | 31.68 | 4.99 | MMIDMDFS | √ | × | 质膜 Plasma membrane |
GuCBL2 | Scaffold00027(+):170105-174365 | 699 | 232 | 26.76 | 4.77 | MVKRDIML | √ | × | 质膜 Plasma membrane |
GuCBL3 | Scaffold00030(-):499662-505101 | 750 | 249 | 28.71 | 4.93 | MPDSDSLF | √ | × | 质膜 Plasma membrane |
GuCBL4 | Scaffold00036(-):366361-373219 | 1 008 | 331 | 37.63 | 9.31 | WLIFQKLK | √ | × | 质膜 Plasma membrane |
GuCBL5 | Scaffold00067(+):227402-231449 | 642 | 213 | 24.36 | 4.67 | MGCFNSKA | √ | √ | 质膜 Plasma membrane |
GuCBL6 | Scaffold00088(-):140793-143426 | 681 | 226 | 25.72 | 4.57 | MVQFLDEL | √ | × | 质膜 Plasma membrane |
GuCBL7 | Scaffold00219(-):429-5651 | 861 | 364 | 41.46 | 5.33 | MDFVASTP | √ | × | 质膜 Plasma membrane |
GuCBL8 | Scaffold00461(-):93781-104251 | 651 | 216 | 24.87 | 4.76 | MGCYCSTS | √ | √ | 质膜 Plasma membrane |
GuCBL9 | Scaffold00669(-):36499-39615 | 717 | 238 | 27.41 | 5.38 | MGCRSSKV | √ | √ | 质膜 Plasma membrane |
GuCBL10 | Scaffold01818(+):19453-23753 | 735 | 269 | 31.13 | 5.35 | MLQQQHRH | √ | × | 质膜 Plasma membrane |
Fig. 1 Chromosomal scaffold distribution of GuCBL genes in G. uralensis GuCBL genes are located on 10 individual scaffolds. Pairs of segmentally duplicated genes are indicated by black lines. Chromosomal scaffolds are showed with different colored circles
Fig. 2 Phylogenetic relationship analysis of the CBL family The CBL proteins of G. uralensis, A. thaliana, and G. max were indicated in red, green, and blue, respectively
Fig. 3 Conserved motif and gene structure analyses of CBL family genes in G. uralensis a: Exon/intron structure analysis of GuCBL genes. Green boxes and black lines represent the exons and introns respectively, and the genomic length is indicated at the bottom. b: Conserved motif analysis of GuCBL proteins
Fig. 4 Multiple alignment and conserved motif analysis of CBL in G. uralensis EF-hand, PFPF-motif, myristoylation site, and serine residue of PFPF-motif are showed in red boxes
Fig. 5 Syntenic analysis of CBL genes in G. uralensis, G. max, and A. thaliana Blue, red, and purple lines represent duplicated CBL pairs in G. uralensis, syntenic relationships of CBL genes between G. uralensis and the other two species of G. max and A. thaliana, and CBL pairs between or inside G. max and A. thaliana
同源基因 Paralogous genes | Ka | Ks | Ka/Ks | 选择压 Selective pressure |
---|---|---|---|---|
GuCBL1-GuCBL7 | 0.2127 | 0.1996 | 1.0656 | Positive selection |
GuCBL3-GuCBL2 | 0.1968 | 0.1674 | 1.1756 | Positive selection |
Table 3 Ka/Ks ratios for homologous CBL genes in G. uralensis
同源基因 Paralogous genes | Ka | Ks | Ka/Ks | 选择压 Selective pressure |
---|---|---|---|---|
GuCBL1-GuCBL7 | 0.2127 | 0.1996 | 1.0656 | Positive selection |
GuCBL3-GuCBL2 | 0.1968 | 0.1674 | 1.1756 | Positive selection |
测试组 Testing group | 测试值Testing value | |||||
---|---|---|---|---|---|---|
Mtb | M1c | M2d | Χ2 | Pe | ||
GuCBL1/GuCBL7 with GmCBL7 | 174 | 16 | 39 | 9.62 | 0.00193 | |
GuCBL3/GuCBL2 with GmCBL6 | 236 | 19 | 5 | 8.27 | 0.00026 |
Table 4 Tajima relative rate tests of homologous CBL gene pairs in G. uralensisa
测试组 Testing group | 测试值Testing value | |||||
---|---|---|---|---|---|---|
Mtb | M1c | M2d | Χ2 | Pe | ||
GuCBL1/GuCBL7 with GmCBL7 | 174 | 16 | 39 | 9.62 | 0.00193 | |
GuCBL3/GuCBL2 with GmCBL6 | 236 | 19 | 5 | 8.27 | 0.00026 |
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