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

Tevfik Hasan Can; Tamer Kuşaksız

Makale detayları

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

Yazarlar:

Tevfik Hasan Can | Tamer Kuşaksız

Yayıncı:

Tokat Gaziosmanpasa University

Ana Başlıklar:

Ziraat Mühendisliği (Diğer)

Dergi:

Gaziosmanpaşa Üniversitesi Ziraat Fakültesi Dergisi Vol.41 Issue 2, pp.86-97

Belge Tipi:

Makale

Yayın Tarihi:

8/2024

Belge Dili:

İngilizce

Document ID (Org No.):

2001326754

pISSN:

1300-2910

Anahtar kelimeler:

Özet:

 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.

 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.

 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.

 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. CmiLEAnın 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-42de 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 90ın 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.

Makale detayları

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

Yazarlar:

Tevfik Hasan Can | Tamer Kuşaksız

Yayıncı:

Tokat Gaziosmanpasa University

Ana Başlıklar:

Ziraat Mühendisliği (Diğer)

Dergi:

Gaziosmanpaşa Üniversitesi Ziraat Fakültesi Dergisi Vol.41 Issue 2, pp.86-97

Belge Tipi:

Makale

Yayın Tarihi:

8/2024

Belge Dili:

İngilizce

Document ID (Org No.):

2001326754

pISSN:

1300-2910

Bioinformatics

LEA genes

LEA proteins

miRNA

Stout Camphor TreeBiyoinformatik

LEA genleri

LEA proteinleri

miRNA

Stout Kafur Ağacı

Sayı

Makale detayları

Yazarlar: Tevfik Hasan Can | Tamer Kuşaksız

Yayıncı: Tokat Gaziosmanpasa University

Ana Başlıklar: Ziraat Mühendisliği (Diğer)

Dergi: Gaziosmanpaşa Üniversitesi Ziraat Fakültesi Dergisi Vol.41 Issue 2, pp.86-97

Belge Tipi: Makale

Yayın Tarihi: 8/2024

Belge Dili: İngilizce

Document ID (Org No.): 2001326754

pISSN: 1300-2910

Sayı

Yazarlar:

Tevfik Hasan Can | Tamer Kuşaksız

Yayıncı:

Tokat Gaziosmanpasa University

Ana Başlıklar:

Ziraat Mühendisliği (Diğer)

Dergi:

Gaziosmanpaşa Üniversitesi Ziraat Fakültesi Dergisi Vol.41 Issue 2, pp.86-97

Belge Tipi:

Makale

Yayın Tarihi:

8/2024

Belge Dili:

İngilizce

Document ID (Org No.):

2001326754

pISSN:

1300-2910