دورية أكاديمية
أعرض في EDS

Computational analysis of potential candidate genes involved in the cold stress response of ten Rosaceae members.

التفاصيل البيبلوغرافية
العنوان: Computational analysis of potential candidate genes involved in the cold stress response of ten Rosaceae members.
المؤلفون: Shafi KM; National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, Karnataka, 560065, India.; The University of Trans-Disciplinary Health Sciences & Technology (TDU), Yelahanka, Bangalore, Karnataka, 560064, India., Sowdhamini R; National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, Karnataka, 560065, India. mini@ncbs.res.in.; Molecular BIophysics Unit, Indian Institute of Science, 560012, Bangalore, India. mini@ncbs.res.in.
المصدر: BMC genomics [BMC Genomics] 2022 Jul 16; Vol. 23 (1), pp. 516. Date of Electronic Publication: 2022 Jul 16.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE
أسماء مطبوعة: Original Publication: London : BioMed Central, [2000-
مواضيع طبية MeSH: Cold-Shock Response*/genetics , Rosaceae*/genetics , Rosaceae*/metabolism, Gene Expression Regulation, Plant ; Multigene Family ; Phylogeny ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Stress, Physiological/genetics ; Transcription Factors/genetics ; Transcription Factors/metabolism
مستخلص: Background: Plant species from Rosaceae family are economically important. One of the major environmental factors impacting those species is cold stress. Although several Rosaceae plant genomes have recently been sequenced, there have been very few research conducted on cold upregulated genes and their promoter binding sites. In this study, we used computational approaches to identify and analyse potential cold stress response genes across ten Rosaceae family members.
Results: Cold stress upregulated gene data from apple and strawberry were used to identify syntelogs in other Rosaceae species. Gene duplication analysis was carried out to better understand the distribution of these syntelog genes in different Rosaceae members. A total of 11,145 popular abiotic stress transcription factor-binding sites were identified in the upstream region of these potential cold-responsive genes, which were subsequently categorised into distinct transcription factor (TF) classes. MYB classes of transcription factor binding site (TFBS) were abundant, followed by bHLH, WRKY, and AP2/ERF. TFBS patterns in the promoter regions were compared among these species and gene families, found to be quite different even amongst functionally related syntelogs. A case study on important cold stress responsive transcription factor family, AP2/ERF showed less conservation in TFBS patterns in the promoter regions. This indicates that syntelogs from the same group may be comparable at the gene level but not at the level of cis-regulatory elements. Therefore, for such genes from the same family, different repertoire of TFs could be recruited for regulation and expression. Duplication events must have played a significant role in the similarity of TFBS patterns amongst few syntelogs of closely related species.
Conclusions: Our study overall suggests that, despite being from the same gene family, different combinations of TFs may play a role in their regulation and expression. The findings of this study will provide information about potential genes involved in the cold stress response, which will aid future functional research of these gene families involved in many important biological processes.
(© 2022. The Author(s).)
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معلومات مُعتمدة: BT/PR40187/BTIS/137/9/2021 Department of Biotechnology, India; BT/PR40187/BTIS/137/9/2021 Department of Biotechnology, India; SB/S2/JC-071/2015 Science and Enginnering Research Board, India
فهرسة مساهمة: Keywords: AP2/ERF family; Cold stress; Gene duplication; Gene promoter; Rosaceae; Syntelog; Transcription factor
المشرفين على المادة: 0 (Plant Proteins)
0 (Transcription Factors)
تواريخ الأحداث: Date Created: 20220716 Date Completed: 20220719 Latest Revision: 20220719
رمز التحديث: 20221213
مُعرف محوري في PubMed: PMC9288012
DOI: 10.1186/s12864-022-08751-x
PMID: 35842574
قاعدة البيانات: MEDLINE
الوصف
تدمد:1471-2164
DOI:10.1186/s12864-022-08751-x