Whole-Genome and Transposed Duplication Contributes to the Expansion and Diversification of <i>TLC</i> Genes in Maize
TLC (TRAM/LAG/CRN8) proteins play important roles in ceramide metabolism and mycotoxin resistance. Herein a comparative genomics analysis of TLCs was performed in 31 plant and 3 species from other kingdoms, with an emphasis mainly on maize. TLCs were conserved across kingdoms and expanded in angiosp...
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doaj-8a8c152744dc4139b952671b591b71572020-11-25T01:55:55ZengMDPI AGInternational Journal of Molecular Sciences1422-00672019-11-012021548410.3390/ijms20215484ijms20215484Whole-Genome and Transposed Duplication Contributes to the Expansion and Diversification of <i>TLC</i> Genes in MaizeWeina Si0Tianlu Hang1Mingyue Guo2Zhen Chen3Qizhi Liang4Longjiang Gu5Ting Ding6National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, ChinaNational Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, ChinaNational Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, ChinaNational Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, ChinaNational Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, ChinaNational Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, ChinaSchool of Plant Protection, Anhui Agricultural University, Hefei 230036, ChinaTLC (TRAM/LAG/CRN8) proteins play important roles in ceramide metabolism and mycotoxin resistance. Herein a comparative genomics analysis of TLCs was performed in 31 plant and 3 species from other kingdoms, with an emphasis mainly on maize. TLCs were conserved across kingdoms and expanded in angiosperms, largely due to whole-genome/segmental duplication (WGD/SD) under purifying selection. Phylogeny reconstruction by maximum-likelihood method uncovered five TLC clades, subsequently named as TRAM/LAG, CLN8, PS-TLC, TM136 and TLCD clades. Each clade of TLCs shared specific transmembrane regions and motif composition. Divisions of conserved motifs to subunits may have occurred in TM136-type TLCs. Focusing on maize, five WGD and two DNA-mediated transposed duplication (TD) pairs were discovered, accounting for 61.11% <i>ZmTLCs</i>. Combined with further expression analysis, significant divergence was found in expression patterns between most maize WGD pairs, indicating subfunctionalization or/and neofunctionalization. Moreover, <i>ZmTLC5</i>, a deduced parental copy in a TD pair, was highly induced under FB<sub>1</sub> and fungus pathogen injection and exhibited potential capacity to respond to environmental stimuli. Additionally, population genetics analysis showed that <i>ZmTLC10</i> in the CLN8-clade may have experienced significant positive selection and differentiated between wild and inbred maize populations. Overall, our results help to decipher the evolutionary history of <i>TLCs</i> in maize and plants, facilitating further functional analysis of them.https://www.mdpi.com/1422-0067/20/21/5484<i>tlc</i> genesgene duplicationsubfunctionalizationmaize |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Weina Si Tianlu Hang Mingyue Guo Zhen Chen Qizhi Liang Longjiang Gu Ting Ding |
spellingShingle |
Weina Si Tianlu Hang Mingyue Guo Zhen Chen Qizhi Liang Longjiang Gu Ting Ding Whole-Genome and Transposed Duplication Contributes to the Expansion and Diversification of <i>TLC</i> Genes in Maize International Journal of Molecular Sciences <i>tlc</i> genes gene duplication subfunctionalization maize |
author_facet |
Weina Si Tianlu Hang Mingyue Guo Zhen Chen Qizhi Liang Longjiang Gu Ting Ding |
author_sort |
Weina Si |
title |
Whole-Genome and Transposed Duplication Contributes to the Expansion and Diversification of <i>TLC</i> Genes in Maize |
title_short |
Whole-Genome and Transposed Duplication Contributes to the Expansion and Diversification of <i>TLC</i> Genes in Maize |
title_full |
Whole-Genome and Transposed Duplication Contributes to the Expansion and Diversification of <i>TLC</i> Genes in Maize |
title_fullStr |
Whole-Genome and Transposed Duplication Contributes to the Expansion and Diversification of <i>TLC</i> Genes in Maize |
title_full_unstemmed |
Whole-Genome and Transposed Duplication Contributes to the Expansion and Diversification of <i>TLC</i> Genes in Maize |
title_sort |
whole-genome and transposed duplication contributes to the expansion and diversification of <i>tlc</i> genes in maize |
publisher |
MDPI AG |
series |
International Journal of Molecular Sciences |
issn |
1422-0067 |
publishDate |
2019-11-01 |
description |
TLC (TRAM/LAG/CRN8) proteins play important roles in ceramide metabolism and mycotoxin resistance. Herein a comparative genomics analysis of TLCs was performed in 31 plant and 3 species from other kingdoms, with an emphasis mainly on maize. TLCs were conserved across kingdoms and expanded in angiosperms, largely due to whole-genome/segmental duplication (WGD/SD) under purifying selection. Phylogeny reconstruction by maximum-likelihood method uncovered five TLC clades, subsequently named as TRAM/LAG, CLN8, PS-TLC, TM136 and TLCD clades. Each clade of TLCs shared specific transmembrane regions and motif composition. Divisions of conserved motifs to subunits may have occurred in TM136-type TLCs. Focusing on maize, five WGD and two DNA-mediated transposed duplication (TD) pairs were discovered, accounting for 61.11% <i>ZmTLCs</i>. Combined with further expression analysis, significant divergence was found in expression patterns between most maize WGD pairs, indicating subfunctionalization or/and neofunctionalization. Moreover, <i>ZmTLC5</i>, a deduced parental copy in a TD pair, was highly induced under FB<sub>1</sub> and fungus pathogen injection and exhibited potential capacity to respond to environmental stimuli. Additionally, population genetics analysis showed that <i>ZmTLC10</i> in the CLN8-clade may have experienced significant positive selection and differentiated between wild and inbred maize populations. Overall, our results help to decipher the evolutionary history of <i>TLCs</i> in maize and plants, facilitating further functional analysis of them. |
topic |
<i>tlc</i> genes gene duplication subfunctionalization maize |
url |
https://www.mdpi.com/1422-0067/20/21/5484 |
work_keys_str_mv |
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