Genome-wide identification and classification of MIKC-type MADS-box genes in Streptophyte lineages and expression analyses to reveal their role in seed germination of orchid
Abstract Background MADS-box genes play crucial roles in plant floral organ formation and plant reproductive development. However, there is still no information on genome-wide identification and classification of MADS-box genes in some representative plant species. A comprehensive investigation of M...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2019-05-01
|
| Series: | BMC Plant Biology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12870-019-1836-5 |
| _version_ | 1828396790340124672 |
|---|---|
| author | Chunmei He Can Si Jaime A. Teixeira da Silva Mingzhi Li Jun Duan |
| author_facet | Chunmei He Can Si Jaime A. Teixeira da Silva Mingzhi Li Jun Duan |
| author_sort | Chunmei He |
| collection | DOAJ |
| description | Abstract Background MADS-box genes play crucial roles in plant floral organ formation and plant reproductive development. However, there is still no information on genome-wide identification and classification of MADS-box genes in some representative plant species. A comprehensive investigation of MIKC-type genes in the orchid Dendrobium officinale is still lacking. Results Here we conducted a genome-wide analysis of MADS-box proteins from 29 species. In total, 1689 MADS-box proteins were identified. Two types of MADS-box genes, termed type I and II, were found in land plants, but not in liverwort. The SQUA, DEF/GLO, AG and SEP subfamilies existed in all the tested flowering plants, while SQUA was absent in the gymnosperm Ginkgo biloba, and no genes of the four subfamilies were found in a charophyte, liverwort, mosses, or lycophyte. This strongly corroborates the notion that clades of floral organ identity genes led to the evolution of flower development in flowering plants. Nine subfamilies of MIKCC genes were present in two orchids, D. officinale and Phalaenopsis equestris, while the TM8, FLC, AGL15 and AGL12 subfamilies may be lost. In addition, the four clades of floral organ identity genes in both orchids displayed a conservative and divergent expression pattern. Only three MIKC-type genes were induced by cold stress in D. officinale while 15 MIKC-type genes showed different levels of expression during seed germination. Conclusions MIKC-type genes were identified from streptophyte lineages, revealing new insights into their evolution and development relationships. Our results show a novel role of MIKC-type genes in seed germination and provide a useful clue for future research on seed germination in orchids. |
| first_indexed | 2024-12-10T08:36:23Z |
| format | Article |
| id | doaj.art-c13499f4aaf44a1181e0ee5001a9b00b |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-10T08:36:23Z |
| publishDate | 2019-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-c13499f4aaf44a1181e0ee5001a9b00b2022-12-22T01:55:58ZengBMCBMC Plant Biology1471-22292019-05-0119111510.1186/s12870-019-1836-5Genome-wide identification and classification of MIKC-type MADS-box genes in Streptophyte lineages and expression analyses to reveal their role in seed germination of orchidChunmei He0Can Si1Jaime A. Teixeira da Silva2Mingzhi Li3Jun Duan4Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of SciencesKey Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of SciencesIndependentGenepioneer Biotechnologies Co. LtdKey Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of SciencesAbstract Background MADS-box genes play crucial roles in plant floral organ formation and plant reproductive development. However, there is still no information on genome-wide identification and classification of MADS-box genes in some representative plant species. A comprehensive investigation of MIKC-type genes in the orchid Dendrobium officinale is still lacking. Results Here we conducted a genome-wide analysis of MADS-box proteins from 29 species. In total, 1689 MADS-box proteins were identified. Two types of MADS-box genes, termed type I and II, were found in land plants, but not in liverwort. The SQUA, DEF/GLO, AG and SEP subfamilies existed in all the tested flowering plants, while SQUA was absent in the gymnosperm Ginkgo biloba, and no genes of the four subfamilies were found in a charophyte, liverwort, mosses, or lycophyte. This strongly corroborates the notion that clades of floral organ identity genes led to the evolution of flower development in flowering plants. Nine subfamilies of MIKCC genes were present in two orchids, D. officinale and Phalaenopsis equestris, while the TM8, FLC, AGL15 and AGL12 subfamilies may be lost. In addition, the four clades of floral organ identity genes in both orchids displayed a conservative and divergent expression pattern. Only three MIKC-type genes were induced by cold stress in D. officinale while 15 MIKC-type genes showed different levels of expression during seed germination. Conclusions MIKC-type genes were identified from streptophyte lineages, revealing new insights into their evolution and development relationships. Our results show a novel role of MIKC-type genes in seed germination and provide a useful clue for future research on seed germination in orchids.http://link.springer.com/article/10.1186/s12870-019-1836-5Flower formationPhylogenetic analysisClassificationGene family expansion |
| spellingShingle | Chunmei He Can Si Jaime A. Teixeira da Silva Mingzhi Li Jun Duan Genome-wide identification and classification of MIKC-type MADS-box genes in Streptophyte lineages and expression analyses to reveal their role in seed germination of orchid BMC Plant Biology Flower formation Phylogenetic analysis Classification Gene family expansion |
| title | Genome-wide identification and classification of MIKC-type MADS-box genes in Streptophyte lineages and expression analyses to reveal their role in seed germination of orchid |
| title_full | Genome-wide identification and classification of MIKC-type MADS-box genes in Streptophyte lineages and expression analyses to reveal their role in seed germination of orchid |
| title_fullStr | Genome-wide identification and classification of MIKC-type MADS-box genes in Streptophyte lineages and expression analyses to reveal their role in seed germination of orchid |
| title_full_unstemmed | Genome-wide identification and classification of MIKC-type MADS-box genes in Streptophyte lineages and expression analyses to reveal their role in seed germination of orchid |
| title_short | Genome-wide identification and classification of MIKC-type MADS-box genes in Streptophyte lineages and expression analyses to reveal their role in seed germination of orchid |
| title_sort | genome wide identification and classification of mikc type mads box genes in streptophyte lineages and expression analyses to reveal their role in seed germination of orchid |
| topic | Flower formation Phylogenetic analysis Classification Gene family expansion |
| url | http://link.springer.com/article/10.1186/s12870-019-1836-5 |
| work_keys_str_mv | AT chunmeihe genomewideidentificationandclassificationofmikctypemadsboxgenesinstreptophytelineagesandexpressionanalysestorevealtheirroleinseedgerminationoforchid AT cansi genomewideidentificationandclassificationofmikctypemadsboxgenesinstreptophytelineagesandexpressionanalysestorevealtheirroleinseedgerminationoforchid AT jaimeateixeiradasilva genomewideidentificationandclassificationofmikctypemadsboxgenesinstreptophytelineagesandexpressionanalysestorevealtheirroleinseedgerminationoforchid AT mingzhili genomewideidentificationandclassificationofmikctypemadsboxgenesinstreptophytelineagesandexpressionanalysestorevealtheirroleinseedgerminationoforchid AT junduan genomewideidentificationandclassificationofmikctypemadsboxgenesinstreptophytelineagesandexpressionanalysestorevealtheirroleinseedgerminationoforchid |