Stout Kafur Ağacında LEA Genlerinin Biyoinformatik Analizi (Cinnamomum micranthum f. Kanehirae)

Year 2024, , 86 - 97, 31.08.2024

Tevfik Hasan Can , Tamer Kuşaksız

https://doi.org/10.55507/gopzfd.1517870

Abstract

LEA proteinleri bitkilerin abiyotik streslere karşı tepkilerinde önemli bir role sahiptir. Lauraceae ailesine ait tıbbi ve aromatik bir bitki olan Cinnamomum micranthum f. Kanehirae veya Stout Kafur ağacının genom dizisi yakın zamanda tamamlanmıştır. Stout Kafur genomunda çalışmalar olmasına rağmen LEA genleri ile alakalı herhangi bir çalışma bulunmamaktadır. Bu nedenle bu çalışmada biyoinformatik araçlar kullanılarak Stout Kafur genomunda yer alan LEA genlerinin genom çapında analizinin yapılması amaçlanmıştır.
Stout Kafur genomunda 57 LEA geni (CmiLEA) tanımlandı. CmiLEA filogenetik analize göre 8 ayrı kümeye ayrılmıştır. CmiLEA'nın subselüler lokalizasyonları incelendiğinde daha çok sitoplazmada lokalize oldukları ve sadece bir miRNA hedefleyen toplam 13 gen tanımlanmıştır. CmiLEA’ da toplam 23 genin yalnızca ekzon bölgelerine sahip olduğu ve intronsuz olduğu tespit edilmiştir. Toplamda 35 korunmuş motif belirlenirken, CmiLEA-42'de yalnızca bir korunmuş motif bulunmuştur. 3B yapı sonuçlarına uygun olarak LEA_2 alt ailesinden CmiLEA-21, CmiLEA-31, CmiLEA-44, CmiLEA-45 ve CmiLEA-57 %90'ın üzerinde doğruluk göstermiştir.
Bu çalışma, Cinnamomum micranthum f. kanehirae bitkisinde LEA genleri ile ilgili yapılmış ilk biyoinformatik çalışma olup, Cinnamomum cinsinde gelecekte ileri fonksiyonel analizler için bir temel oluşturabileceği düşünülmektedir.

Keywords

Biyoinformatik, LEA genleri, LEA proteinleri, miRNA, Stout Kafur Ağacı

Bioinformatic Analysis of LEA Genes in Stout Camphor Tree (Cinnamomum micranthum f. Kanehirae)

Abstract

LEA proteins have an important role in the response of plants to abiotic stresses. Cinnamomum micranthum f. kanehirae, a medicinal and aromatic plant belonging to the Lauraceae family. The genome sequence of the Kanehirae or Stout Camphor tree was recently completed. Although there are studies on its genome, there are no studies on LEA genes.
57 LEA genes (CmiLEA) were identified in the Stout Camphor genome. CmiLEA was divided into 8 distinct clusters based on phylogenetic analysis. When the subcellular localizations of CmiLEA were examined, they were found to be localized mostly in the cytoplasm. A total of 13 genes targeting only one miRNA were identified. In CmiLEA, a total of 23 genes were found to have only exon regions and no introns. In total, 35 conserved motifs were identified, while there was only one conserved motif in CmiLEA-42. Consistent with the 3D structure results, CmiLEA-21, CmiLEA-31, CmiLEA-44, CmiLEA-45, and CmiLEA-57 from the LEA-2 subfamily showed over 90% accuracy.
The present study was the first in-silico analysis of LEA genes in Cinnamomum micranthum f. Kanehirae. It is thought that it may form a base for advanced functional analysis in Cinnamomum in future.

Keywords

Bioinformatics, LEA genes, LEA proteins, miRNA, Stout Camphor Tree

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