De novo transcriptome assembly reveals three alternative oxidase encoding genes in Nymphaea alba L.

Year 2022, Volume: 10 Issue: 1, 285 - 299, 31.01.2022

Ercan Selçuk Ünlü , Gülgez Gökçe Yıldız

https://doi.org/10.29130/dubited.914845

Abstract

Water lilies are aquatic, ornamental and economically valuable plants classified under Nymphaea genus. Nymphaea alba L., white water lily, has a special focus since it is a member of basal angiosperms. Alternative oxidase (AOX) proteins are the terminal oxidases in the electron transport chain of plants. Identification of alternative oxidase encoding genes for basal angiosperms is important to increase the quality of phylogenetic studies. However, AOX encoding genes were yet to be discovered for N. alba. In this study, we aimed to identify alternative oxidase encoding genes in N. alba by performing transcriptome analysis. Annotation of 272,934 unigenes with Trinotate tool revealed 77 transcripts with AOX domains characterized in known alternative oxidases. Blast analysis of these 77 sequences with known AOX proteins revealed three distinct AOX genes (AOX1, AOX2 and AOX4) in N. alba. After in silico subcellular localization analysis of three identified AOX proteins, AOX1, AOX2 are predicted as mitochondrial while AOX4 is a plastidic alternative oxidase protein. Template-based structural modeling results showed that all identified proteins are statistically similar to known structure models of corresponding AOXs.

Keywords

AOX, Abant Lake, RNA-Seq, Water lilies

Supporting Institution

Bolu Abant İzzet Baysal Üniversitesi

Project Number

2014.03.03.714

Thanks

This study was financially supported by Bolu Abant İzzet Baysal University [Grant no: 2014.03.03.714]. We also thank Ph.D. students Özge KAYA, Ömer Can ÜNÜVAR, and Yunus ŞAHİN for helping through field sampling

De Novo Transkriptom Birleştirme Analizi Nymphaea alba L. Türünde Üç Alternatif Oksidaz Kodlayan Gen Olduğunu Göstermektedir

Abstract

Nilüfer bitkileri ekonomik değeri yüksek sucul süs bitkileri olup Nymphaea ailesi altında sınıflandırılmaktadırlar. Nymphaea alba L. (Beyaz nilüfer) bazal angiospermlerin bir üyesi olduklarından özel bir öneme sahiptir. Alternatif oksidaz kodlayan genlerin bazal angiospermlerde belirlenmesi filogenetik çalışmaların kalitesini artırmak için önemlidir. N. alba için AOX sentezinden sorumlu genler henüz tanımlanmamıştır. Bu çalışmada transkriptom analizi uygulamaları ile N. alba türünde AOX sentezinden sorumlu genlerin tanımlanmasını amaçlanmıştır. Trinotate aracılığı ile 272934 unigenin tanımlaması yapılarak, bilinen alternatif oksidazlarda karakterize edilmiş AOX domainlerini içeren 77 transkriptin dizisi ortaya çıkarılmıştır. Bu 77 transkriptin bilinen AOX proteinlerine karşı Blast analizleri ile N. alba türüne ait üç ayrı AOX geni (AOX1, AOX2 and AOX4) tespit edilmiştir. In silico hücre içi lokalizasyon analizine göre AOX1 ve AOX2 proteinleri mitokondriyal, AOX4 ise plastidik alternatif oksidaz proteinidir. Şablon bazlı yapısal modelleme sonuçları, tanımlanmış bu proteinlerin model verilerinin, başka türlerde karşılık geldiği AOX proteinlerinin bilinen yapı modellerine istatistiksel olarak benzer olduğunu göstermiştir.

Keywords

AOX, Abant Gölü, RNA-Seq, Nilüfergiller

Project Number

2014.03.03.714

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