De novo genome assembly of two tomato ancestors, Solanum pimpinellifolium and Solanum
   lycopersicum var. cerasiforme, by long-read sequencing

Takei, Hitomi; Shirasawa, Kenta; Kuwabara, Kosuke; Toyoda, Atsushi; Matsuzawa, Yuma; Iioka, Shinji; Ariizumi, Tohru

doi:10.1093/dnares/dsaa029

Cited by 26 publications

(17 citation statements)

References 23 publications

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“…Among the 40 SbTH genes, 8 (20.0%) contained the GT1 domain, 23 (57.5%) contained the Myb_DNA-binding domain and 9 (22.5%) contained both GT1 domain and Myb DNA-binding domain. The ratio of SbTH genes to total genes in the S. bicolor genome was about 0.12% [ 18 ], which is similar to that of Arabidopsis (0.11%) [ 19 , 20 ], soybean (0.14%) [ 21 , 22 ], and rice (0.10%) [ 23 , 24 ] but more that than of tomato (0.05%) [ 12 , 25 ], chrysanthemum (0.04%) [ 26 , 27 ], wheat (0.08%) [ 28 , 29 ], and buckwheat (0.06%) [ 30 , 31 ].…”

Section: Resultsmentioning

confidence: 97%

Genome-wide identification and expression profile analysis of trihelix transcription factor family genes in response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench]

Duan

Zhang

et al. 2021

BMC Genomics

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Background Transcription factors, including trihelix transcription factors, play vital roles in various growth and developmental processes and in abiotic stress responses in plants. The trihelix gene has been systematically studied in some dicots and monocots, including Arabidopsis, tomato, chrysanthemum, soybean, wheat, corn, rice, and buckwheat. However, there are no related studies on sorghum. Results In this study, a total of 40 sorghum trihelix (SbTH) genes were identified based on the sorghum genome, among which 34 were located in the nucleus, 5 in the chloroplast, 1 (SbTH38) in the cytoplasm, and 1 (SbTH23) in the extracellular membrane. Phylogenetic analysis of the SbTH genes and Arabidopsis and rice trihelix genes indicated that the genes were clustered into seven subfamilies: SIP1, GTγ, GT1, GT2, SH4, GTSb8, and orphan genes. The SbTH genes were located in nine chromosomes and none on chromosome 10. One pair of tandem duplication gene and seven pairs of segmental duplication genes were identified in the SbTH gene family. By qPCR, the expression of 14 SbTH members in different plant tissues and in plants exposed to six abiotic stresses at the seedling stage were quantified. Except for the leaves in which the genes were upregulated after only 2 h exposure to high temperature, the 12 SbTH genes were significantly upregulated in the stems of sorghum seedlings after 24 h under the other abiotic stress conditions. Among the selected genes, SbTH10/37/39 were significantly upregulated, whereas SbTH32 was significantly downregulated under different stress conditions. Conclusions In this study, we identified 40 trihelix genes in sorghum and found that gene duplication was the main force driving trihelix gene evolution in sorghum. The findings of our study serve as a basis for further investigation of the functions of SbTH genes and providing candidate genes for stress-resistant sorghum breeding programmes and increasing sorghum yield.

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Section: Resultsmentioning

confidence: 97%

Genome-wide identification and expression profile analysis of trihelix transcription factor family genes in response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench]

Duan

Zhang

et al. 2021

BMC Genomics

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“…The longest transcripts of each protein-coding gene in H. hamabo and other carefully selected species ( Arabidopsis thaliana [ 72 ] , Corchorus olitorius [ 73 ] , Gossypium raimondii [ 74 ] , H. syriacus [ 34 ] , Theobroma cacao [ 75 ] , Bombax ceiba [ 76 ] , Durio zibethinus [ 77 ] , H. cannabinus [ 17 ] , Populus trichocarpa [ 78 ] , Vitis vinifera [ 79 ] , Corchorus capsularis [ 80 ] , Glycine max [ 81 ] and Solanum lycopersicum [ 82 ]) were used to cluster the gene families. All longest transcripts were extracted using a python script from the OrthoFinder repository at Github ( https://github.com/davidemms/OrthoFinder ).…”

Section: Methodsmentioning

confidence: 99%

The genome of Hibiscus hamabo reveals its adaptation to saline and waterlogged habitat

Wang

Xue

et al. 2022

Horticulture Research

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Hibiscus hamabo is a semi-mangrove species with strong tolerance to salt and waterlogging stress. However, the molecular basis and mechanisms that underlie this strong adaptability to harsh environments remain poorly understood. Here, we assembled a high-quality, chromosome-level genome of this semi-mangrove plant and analyzed its transcriptome under different stress treatments to reveal regulatory responses and mechanisms. Our analyses suggested that H. hamabo has undergone two recent successive polyploidy events, a whole-genome duplication followed by a whole-genome triplication, resulting in an unusually large gene number (107,309 genes). Comparison of the H. hamabo genome with that of its close relative Hibiscus cannabinus, which has not experienced a recent WGT, indicated that genes associated with high stress resistance have been preferentially preserved in the H. hamabo genome, suggesting an underlying association between polyploidy and stronger stress resistance. Transcriptomic data indicated that genes in the roots and leaves responded differently to stress. In roots, genes that regulate ion channels involved in biosynthetic and metabolic processes responded quickly to adjust the ion concentration and provide metabolic products to protect root cells, whereas no such rapid response was observed from genes in leaves. Using co-expression networks, potential stress resistance genes were identified for use in future functional investigations. The genome sequence, along with several transcriptome datasets, provide insights into genome evolution and the mechanism of salt and waterlogging tolerance in H. hamabo, suggesting the importance of polyploidization for environmental adaptation.

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“…In this study, a total of 47 trihelix genes were identified in C. quinoa genome, which is in agreement with the studies on tomato, sorghum, and rice [ 9 , 21 , 22 ]. The CqTH genes account for 0.11% of the total genes in the C. quinoa genome [ 18 ], which is similar to A. thaliana (0.11%) [ 23 ], G. max (0.14%) [ 24 ], and O. sativa (0.10%) [ 25 ] and higher than that of S. lycopersicum (0.05%) [ 26 ], Chrysanthemum (0.04%) [ 27 ], Triticum (0.08%) [ 28 ], and F. tataricum (0.06%) [ 29 ]. Trihelix genes were initially grouped into three separate subfamilies, namely GTα, GTβ, and GTγ [ 16 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification, phylogenetic analysis, and expression profiles of trihelix transcription factor family genes in quinoa (Chenopodium quinoa Willd.) under abiotic stress conditions

Fan

Zhou

et al. 2022

BMC Genomics

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Background The trihelix family of transcription factors plays essential roles in the growth, development, and abiotic stress response of plants. Although several studies have been performed on the trihelix gene family in several dicots and monocots, this gene family is yet to be studied in Chenopodium quinoa (quinoa). Results In this study, 47 C. quinoa trihelix (CqTH) genes were in the quinoa genome. Phylogenetic analysis of the CqTH and trihelix genes from Arabidopsis thaliana and Beta vulgaris revealed that the genes were clustered into five subfamilies: SIP1, GTγ, GT1, GT2, and SH4. Additionally, synteny analysis revealed that the CqTH genes were located on 17 chromosomes, with the exception of chromosomes 8 and 11, and 23 pairs of segmental duplication genes were detected. Furthermore, expression patterns of 10 CqTH genes in different plant tissues and at different developmental stages under abiotic stress and phytohormone treatment were examined. Among the 10 genes, CqTH02, CqTH25, CqTH18, CqTH19, CqTH25, CqTH31, and CqTH36, were highly expressed in unripe achenes 21 d after flowering and in mature achenes compared with other plant tissues. Notably, the 10 CqTH genes were upregulated in UV-treated leaves, whereas CqTH36 was consistently upregulated in the leaves under all abiotic stress conditions. Conclusions The findings of this study suggest that gene duplication could be a major driver of trihelix gene evolution in quinoa. These findings could serve as a basis for future studies on the roles of CqTH transcription factors and present potential genetic markers for breeding stress-resistant and high-yielding quinoa varieties.

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De novo genome assembly of two tomato ancestors, Solanum pimpinellifolium and Solanum lycopersicum var. cerasiforme, by long-read sequencing

Cited by 26 publications

References 23 publications

Genome-wide identification and expression profile analysis of trihelix transcription factor family genes in response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench]

Genome-wide identification and expression profile analysis of trihelix transcription factor family genes in response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench]

The genome of Hibiscus hamabo reveals its adaptation to saline and waterlogged habitat

Genome-wide identification, phylogenetic analysis, and expression profiles of trihelix transcription factor family genes in quinoa (Chenopodium quinoa Willd.) under abiotic stress conditions

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