Comprehensive analysis of the flowering genes in Chinese cabbage and examination of evolutionary pattern of CO-like genes in plant kingdom

Song, Xiaoming; Duan, Weike; Huang, Zhinan; Liu, Gaofeng; Wu, Peng; Liu, Tongkun; Li, Ying; Hou, Xilin

doi:10.1038/srep14631

Cited by 46 publications

(49 citation statements)

References 84 publications

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“…The "L"and "D" indicates the loss and duplication, respectively. The number after "L" and "D" represents the number of genes families of B. rapa and B. napus, such as BES1, AP2/ERF, CO-Like, bHLH, BES1, HSF, GARS, and cold-related genes [36][37][38][39][40][41][42][43][44][45][46]. The methods, techniques, and experiences of these studies laid the foundation for an in-depth analysis of TLP gene family.…”

Section: Discussionmentioning

confidence: 99%

Identification, evolution and expression analyses of whole genome-wide TLP gene family in Brassica napus

Wang

et al. 2020

BMC Genomics

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Background: Brassica is a very important genus of Brassicaceae, including many important oils, vegetables, forage crops, and ornamental horticultural plants. TLP family genes play important regulatory roles in the growth and development of plants. Therefore, this study used a bioinformatics approach to conduct the systematic comparative genomics analysis of TLP gene family in B. napus and other three important Brassicaceae crops. Results: Here, we identified a total of 29 TLP genes from B. napus genome, and they distributed on 16 chromosomes of B. napus. The evolutionary relationship showed that these genes could be divided into six groups from Group A to F. We found that the gene corresponding to Arabidopsis thaliana AT1G43640 was completely lost in B. rapa, B. oleracea and B. napus after whole genome triplication. The gene corresponding to AT1G25280 was retained in all the three species we analysed, belonging to 1:3:6 ratios. Our analyses suggested that there was a selective loss of some genes that might be redundant after genome duplication. This study proposed that the TLP genes in B. napus did not directly expansion compared with its diploid parents B. rapa, and B. oleracea. Instead, an indirect expansion of TLP gene family occurred in its two diploid parents. In addition, the study further utilized RNA-seq to detect the expression pattern of TLP genes between different tissues and two subgenomes. Conclusions: This study systematically conducted the comparative analyses of TLP gene family in B. napus, discussed the loss and expansion of genes after genome duplication. It provided rich gene resources for exploring the molecular mechanism of TLP gene family. Meanwhile, it provided guidance and reference for the research of other gene families in B. napus.

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Section: Discussionmentioning

confidence: 99%

Identification, evolution and expression analyses of whole genome-wide TLP gene family in Brassica napus

Wang

et al. 2020

BMC Genomics

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“…The major Brassica crops include three diploid species (B. rapa, B. nigra, and B. oleracea) and three allotetraploid species (B. napus, B. juncea, and B. carinata) [57][58][59]. With the completion of the genome sequences of these Brassica species, the genetic and molecular functions of interesting genes, such as AP2/ERF, MYB, BOR, CO-like, and GRAS genes, have been widely studied in B. rapa and B. napus [60][61][62][63][64][65]. PHT genes encode H 2 PO 4− /H + co-transporters that are responsible for the absorption and transport of phosphorus in plant roots.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Analysis of Phosphorus Transporter Genes in Brassica and Their Roles in Heavy Metal Stress Tolerance

Wan

Wang

Xia

et al. 2020

IJMS

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Phosphorus transporter (PHT) genes encode H2PO4−/H+ co-transporters that absorb and transport inorganic nutrient elements required for plant development and growth and protect plants from heavy metal stress. However, little is known about the roles of PHTs in Brassica compared to Arabidopsis thaliana. In this study, we identified and extensively analyzed 336 PHTs from three diploid (B. rapa, B. oleracea, and B. nigra) and two allotetraploid (B. juncea and B. napus) Brassica species. We categorized the PHTs into five phylogenetic clusters (PHT1–PHT5), including 201 PHT1 homologs, 15 PHT2 homologs, 40 PHT3 homologs, 54 PHT4 homologs, and 26 PHT5 homologs, which are unevenly distributed on the corresponding chromosomes of the five Brassica species. All PHT family genes from Brassica are more closely related to Arabidopsis PHTs in the same vs. other clusters, suggesting they are highly conserved and have similar functions. Duplication and synteny analysis revealed that segmental and tandem duplications led to the expansion of the PHT gene family during the process of polyploidization and that members of this family have undergone purifying selection during evolution based on Ka/Ks values. Finally, we explored the expression profiles of BnaPHT family genes in specific tissues, at various developmental stages, and under heavy metal stress via RNA-seq analysis and qRT-PCR. BnaPHTs that were induced by heavy metal treatment might mediate the response of rapeseed to this important stress. This study represents the first genome-wide analysis of PHT family genes in Brassica species. Our findings improve our understanding of PHT family genes and provide a basis for further studies of BnaPHTs in plant tolerance to heavy metal stress.

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“…The topranked rice hit was used to construct the CRG library combined with 115 Arabidopsis CRGs. Then, homologous CRGs in other species were identified through comparison with the Arabidopsis and rice CRG library by using the Blastp program (E-value < 1 × 10 −10 , identity > 60%) according to a previous report 60 . The Pfam (v32.0, http:// pfam.xfam.org) database and a related Perl script were used to identify the NBS gene family 61 .…”

Section: Identification and Characterization Of Crgs And Nbs Genesmentioning

confidence: 99%

Preferential gene retention increases the robustness of cold regulation in Brassicaceae and other plants after polyploidization

et al. 2020

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Cold stress profoundly affects plant growth and development and is a key factor affecting the geographic distribution and evolution of plants. Plants have evolved adaptive mechanisms to cope with cold stress. Here, through the genomic analysis of Arabidopsis, three Brassica species and 17 other representative species, we found that both cold-related genes (CRGs) and their collinearity were preferentially retained after polyploidization followed by genome instability, while genome-wide gene sets exhibited a variety of other expansion mechanisms. The coldrelated regulatory network was increased in Brassicaceae genomes, which were recursively affected by polyploidization. By combining our findings regarding the selective retention of CRGs from this ecological genomics study with the available knowledge of cold-induced chromosome doubling, we hypothesize that cold stress may have contributed to the success of polyploid plants through both increasing polyploidization and selectively maintaining CRGs during evolution. This hypothesis requires further biological and ecological exploration to obtain solid supporting evidence, which will potentially contribute to understanding the generation of polyploids and to the field of ecological genomics.

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Comprehensive analysis of the flowering genes in Chinese cabbage and examination of evolutionary pattern of CO-like genes in plant kingdom

Cited by 46 publications

References 84 publications

Identification, evolution and expression analyses of whole genome-wide TLP gene family in Brassica napus

Identification, evolution and expression analyses of whole genome-wide TLP gene family in Brassica napus

Genome-Wide Analysis of Phosphorus Transporter Genes in Brassica and Their Roles in Heavy Metal Stress Tolerance

Preferential gene retention increases the robustness of cold regulation in Brassicaceae and other plants after polyploidization

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