Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus jujuba) by in silico Methods

Yusuf Ceylan; Kevser Betül Ceylan; Yasemin Çelik Altunoğlu; Mehmet Cengiz Baloğlu

doi:10.17475/kastorman.1049963

EN TR

Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus jujuba) by in silico Methods

Abstract

Aim of study: It was aimed to identify and characterize Hsp genes in jujube genome using genomics methods. Material and method: Protein sequences of jujube Hsp genes were obtained from NCBI databases. GSDS program was used to detect of exon-intron sites. To define the conserved motifs and estimated 3D-structures, Hsp proteins were used in the MEME-SUITE and PHYRE2 program, respectively. miRNAs targeting ZjuHsp transcripts were identified using the psRNATarget Server database. The gene annotations of Hsp proteins were presented by Blast2GO program. Sequence alignment was performed with ClustalW software, and then the phylogenetic tree was drawn using MEGAX program. Main results: A total of 474 genes were defined in the jujube genome. The amino acid length of the Hsp proteins changes from 75 aa to 2577 aa. The estimated 3-D structure of the ZjuHsp proteins revealed the dominance of the α-helix structure. Phylogenetic tree was constructed to detect evolutionary relationships revealed the eight major groups of the ZjuHsp100 and ZjuHsp60. ZjuHsp proteins could be mainly found in cell parts, membranes, and organelles. It was determined that the ZjuHsp100 genes was targeted by 313 miRNAs. Highlights: This study helps the researchers who would like to comparative and functional genomic studies.

Keywords

Heat Shock Proteins (Hsp), Ziziphus jujuba, Genome Wide Identification, Gene Ontology Analysis, Phylogenetic Tree

Hünnap Genomunda (Ziziphus jujuba) Isı Şoku Protein Ailelerinin in silico Yöntemler ile Genomik ve Fonksiyonel Karakterizasyonu

Abstract

Çalışmanın amacı : Bu çalıĢmada, genomic yöntemler kullanarak hünnap genomunda yer alan Hsp genlerini tanımlamak ve karakterize etmek amaçlanmıĢtır. Materyal ve yöntem : NCBI veritabanı kullanılarak Hsp genlerinin protein dizileri elde edilmiĢtir. Genlerin ekzon-intron bölgelerinin tespiti, GSDS program ile yapılmıĢtır. Hsp proteinlerinin korunmuĢ motiflerini ve tahmini üç boyutlu yapılarını tanımlamak için sırasıyla MEME-SUITE ve PHYRE2 programı kullanılmıĢtır. Hsp transkriptlerini hedefleyen miRNA'lar, psRNATarget Server veritabanı kullanılarak tanımlanmıĢtır. Hsp proteinlerinin moleküler fonksiyonu, hücresel bileĢeni ve biyolojik fonksiyonları Blast2GO program ile sunulmuĢtur. Hsp proteinlerinin evrimsel iliĢkilerini belirlemek amacı ile ClustalW yazılımı ile dizi hizalaması yapılmıĢ ve ardından MEGAX program ile filogenetik ağaç çizilmiĢtir. Temel sonuçlar: Hünnap genomunda toplam 474 gen tanımlanmıĢ ve genler çoğunlukla 1. ve 2. kromozomda dağılım göstermiĢtir. Hsp proteinlerinin amino asit uzunluğu 75 aa (ZjuHsp100-117) ile 2577 aa (ZjuHsp40-104 ve ZjuHsp40-157) arasında değiĢim göstermiĢtir. ZjuHsp proteinlerinin tahmini üç boyutlu yapısında α-sarmal yapısının baskın olduğu görülmüĢtür. Proteinlerin evrimsel iliĢkilerini saptamak için oluĢturulan filogenetik ağaçta, ZjuHsp100 ve ZjuHsp60 grup proteinlerin sekiz ana gruba ayrıldığı gözlenmiĢtir. ZjuHsp proteinlerinin esas olarak hücre kısımlarında, zarlarda, ve organellerde bulunduğu tespit edilmiĢtir. ZjuHsp transkriptlerini hedef alan miRNA'lardan 313'ünün ZjuHsp100 genlerini hedeflediği bulunmuĢtur. Araştırma vurguları : Bu çalıĢma, karĢılaĢtırmalı ve fonksiyonel genomic çalıĢmalar yapmak isteyen araĢtırmacılara yardımcı olmaktadır. Anahtar Kelimeler: Isı şoku Proteinleri (Hsp), Ziziphus jujuba, Genom Analizi, Gen Ontoloji Analizi, Filogenetik Ağaç

Keywords

Ziziphus jujuba, Genom Analizi, Gen Ontoloji Analizi, Filogenetik Ağaç, Isı şoku Proteinleri (Hsp), Ziziphus jujuba, Genom Analizi, Gen Ontoloji Analizi, Filogenetik Ağaç

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Details

Primary Language

English

Subjects

-

Journal Section

Research Article

Authors

Yusuf Ceylan
Türkiye

Kevser Betül Ceylan This is me
Türkiye

Yasemin Çelik Altunoğlu This is me
Türkiye

Mehmet Cengiz Baloğlu ^* This is me
Türkiye

Publication Date

December 31, 2021

Submission Date

July 26, 2021

Acceptance Date

October 11, 2021

Published in Issue

Year 2021 Volume: 21 Number: 3

DOI

https://doi.org/10.17475/kastorman.1049963

IZ

https://izlik.org/JA67BU69PF

APA

Ceylan, Y., Ceylan, K. B., Çelik Altunoğlu, Y., & Baloğlu, M. C. (2021). Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus jujuba) by in silico Methods. Kastamonu University Journal of Forestry Faculty, 21(3), 277-294. https://doi.org/10.17475/kastorman.1049963

AMA

1.Ceylan Y, Ceylan KB, Çelik Altunoğlu Y, Baloğlu MC. Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus jujuba) by in silico Methods. Kastamonu University Journal of Forestry Faculty. 2021;21(3):277-294. doi:10.17475/kastorman.1049963

Chicago

Ceylan, Yusuf, Kevser Betül Ceylan, Yasemin Çelik Altunoğlu, and Mehmet Cengiz Baloğlu. 2021. “Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus Jujuba) by in Silico Methods”. Kastamonu University Journal of Forestry Faculty 21 (3): 277-94. https://doi.org/10.17475/kastorman.1049963.

EndNote

Ceylan Y, Ceylan KB, Çelik Altunoğlu Y, Baloğlu MC (December 1, 2021) Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus jujuba) by in silico Methods. Kastamonu University Journal of Forestry Faculty 21 3 277–294.

IEEE

[1]Y. Ceylan, K. B. Ceylan, Y. Çelik Altunoğlu, and M. C. Baloğlu, “Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus jujuba) by in silico Methods”, Kastamonu University Journal of Forestry Faculty, vol. 21, no. 3, pp. 277–294, Dec. 2021, doi: 10.17475/kastorman.1049963.

ISNAD

Ceylan, Yusuf - Ceylan, Kevser Betül - Çelik Altunoğlu, Yasemin - Baloğlu, Mehmet Cengiz. “Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus Jujuba) by in Silico Methods”. Kastamonu University Journal of Forestry Faculty 21/3 (December 1, 2021): 277-294. https://doi.org/10.17475/kastorman.1049963.

JAMA

1.Ceylan Y, Ceylan KB, Çelik Altunoğlu Y, Baloğlu MC. Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus jujuba) by in silico Methods. Kastamonu University Journal of Forestry Faculty. 2021;21:277–294.

MLA

Ceylan, Yusuf, et al. “Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus Jujuba) by in Silico Methods”. Kastamonu University Journal of Forestry Faculty, vol. 21, no. 3, Dec. 2021, pp. 277-94, doi:10.17475/kastorman.1049963.

Vancouver

1.Yusuf Ceylan, Kevser Betül Ceylan, Yasemin Çelik Altunoğlu, Mehmet Cengiz Baloğlu. Genomic and Functional Characterization of Heat Shock Protein Families in Jujube Genome (Ziziphus jujuba) by in silico Methods. Kastamonu University Journal of Forestry Faculty. 2021 Dec. 1;21(3):277-94. doi:10.17475/kastorman.1049963

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