TreeBASE Search-Matrices for study 27434

@ARTICLE{TreeBASE2Ref31563, author = {Taehoon Kim and Shafina Samraj and Juan Jimenez and Celina Gomez and Tie Liu and Kevin Begcy}, title = {Surveying the lettuce genome: Genome-wide identification of Hsfs and Hsps in response to UV and high light stress}, year = {2020}, keywords = {Lettuce, heat shock factors, heat shock proteins, gene duplication, light conditions}, doi = {}, url = {http://}, pmid = {}, journal = {BMC Plant Biology}, volume = {}, number = {}, pages = {}, abstract = {[Background] Heat shock factors (Hsfs) and Heat shock proteins (Hsps) belong to an essential group of molecular regulators involved in controlling cellular processes under normal and stress conditions. The role of Hsfs and Hsps is well known in model plant species under diverse stress conditions. However, in lettuce (Lactuca sativa), a highly consumed vegetable crop grown in the field and in hydroponic systems, the role of these gene families in response to artificial light is not well characterized. [Results] Using a genome-wide analysis approach, we identified 32 Hsfs and 22 small heat shock proteins (LsHsps) in lettuce, some of which do not have orthologous in Arabidopsis, poplar, and rice. LsHsp60s, LsHsp90s, and LsHsp100s are highly conserved among dicot and monocot species. Surprisingly, LsHsp70s have three times more members than Arabidopsis and two times more than rice. Genome triplication might have contributed to the increased number of LsHsp70s genes. Chromosomal distribution analysis shows larger tandem repeats of LsHsp70s genes in Chr1, Chr7, Chr8, and Chr9. At the transcriptional level, some genes of the LsHsfs, LsHsps, LsHsp60s, and LsHsp70s families were highly responsive to UV and high light stress, in contrast of LsHsp90s and LsHsp100s which did not respond to a light stimulus. [Conclusions] Our genome-wide analysis provides a detail identification of Hsfs and Hsps in lettuce. Chromosomal location and syntenic region analysis together with our transcriptional analysis under different light conditions provide candidate genes for breeding programs aiming to produce lettuce varieties able to grow healthy under hydroponic systems that use artificial light. } }

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Matrices for Study 27434

Citation title: "Surveying the lettuce genome: Genome-wide identification of Hsfs and Hsps in response to UV and high light stress".

Study name: "Surveying the lettuce genome: Genome-wide identification of Hsfs and Hsps in response to UV and high light stress".

This study is part of submission 27434 (Status: Published).

Matrices

ID	Matrix Title	Description	Data type	NTAX	NCHAR	Taxa
M57451	Lactuca sativa Athaliana Hsf	Protein alignment of lettuce and Arabidopsis Hsf genes using MUSCLE	Amino Acid	53	676	View Taxa
M57449	Lactuca sativa Athaliana Hsp70	Protein alignment of lettuce and Arabidopsis Hsp70 genes using MUSCLE	Amino Acid	82	1159	View Taxa
M57450	Lactuca sativa Athaliana Hsp90	Protein alignment of lettuce and Arabidopsis Hsp90 genes using MUSCLE	Amino Acid	14	891	View Taxa
M57448	Lactuca sativa Athaliana Hsp100	Protein alignment of lettuce and Arabidopsis Hsp100 genes using MUSCLE	Amino Acid	15	1101	View Taxa
M57453	Lactuca sativa Athaliana sHsp	Protein alignment of lettuce and Arabidopsis sHsp genes using MUSCLE	Amino Acid	51	475	View Taxa
M57452	Lactuca sativa Athaliana Hsp60	Protein alignment of lettuce and Arabidopsis Hsp60 genes using MUSCLE	Amino Acid	40	829	View Taxa