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

Ercan Selçuk Ünlü; Gülgez Gökçe Yıldız

doi:10.29130/dubited.914845

TR EN

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

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

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

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Details

Primary Language

English

Subjects

Engineering

Journal Section

Research Article

Authors

Ercan Selçuk Ünlü ^*
0000-0003-0097-1125
Türkiye

Gülgez Gökçe Yıldız This is me
0000-0002-4095-6619
Türkiye

Publication Date

January 31, 2022

Submission Date

April 12, 2021

Acceptance Date

August 18, 2021

Published in Issue

Year 2022 Volume: 10 Number: 1

DOI

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

IZ

https://izlik.org/JA44BD86CC

APA

Ünlü, E. S., & Yıldız, G. G. (2022). De novo transcriptome assembly reveals three alternative oxidase encoding genes in Nymphaea alba L. Duzce University Journal of Science and Technology, 10(1), 285-299. https://doi.org/10.29130/dubited.914845

AMA

1.Ünlü ES, Yıldız GG. De novo transcriptome assembly reveals three alternative oxidase encoding genes in Nymphaea alba L. DUBİTED. 2022;10(1):285-299. doi:10.29130/dubited.914845

Chicago

Ünlü, Ercan Selçuk, and Gülgez Gökçe Yıldız. 2022. “De Novo Transcriptome Assembly Reveals Three Alternative Oxidase Encoding Genes in Nymphaea Alba L”. Duzce University Journal of Science and Technology 10 (1): 285-99. https://doi.org/10.29130/dubited.914845.

EndNote

Ünlü ES, Yıldız GG (January 1, 2022) De novo transcriptome assembly reveals three alternative oxidase encoding genes in Nymphaea alba L. Duzce University Journal of Science and Technology 10 1 285–299.

IEEE

[1]E. S. Ünlü and G. G. Yıldız, “De novo transcriptome assembly reveals three alternative oxidase encoding genes in Nymphaea alba L”., DUBİTED, vol. 10, no. 1, pp. 285–299, Jan. 2022, doi: 10.29130/dubited.914845.

ISNAD

Ünlü, Ercan Selçuk - Yıldız, Gülgez Gökçe. “De Novo Transcriptome Assembly Reveals Three Alternative Oxidase Encoding Genes in Nymphaea Alba L”. Duzce University Journal of Science and Technology 10/1 (January 1, 2022): 285-299. https://doi.org/10.29130/dubited.914845.

JAMA

1.Ünlü ES, Yıldız GG. De novo transcriptome assembly reveals three alternative oxidase encoding genes in Nymphaea alba L. DUBİTED. 2022;10:285–299.

MLA

Ünlü, Ercan Selçuk, and Gülgez Gökçe Yıldız. “De Novo Transcriptome Assembly Reveals Three Alternative Oxidase Encoding Genes in Nymphaea Alba L”. Duzce University Journal of Science and Technology, vol. 10, no. 1, Jan. 2022, pp. 285-99, doi:10.29130/dubited.914845.

Vancouver

1.Ercan Selçuk Ünlü, Gülgez Gökçe Yıldız. De novo transcriptome assembly reveals three alternative oxidase encoding genes in Nymphaea alba L. DUBİTED. 2022 Jan. 1;10(1):285-99. doi:10.29130/dubited.914845

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

Abstract

Keywords

Project Number

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

Abstract

Keywords

Supporting Institution

Project Number

Thanks

References

Details

Primary Language

Subjects

Journal Section

Authors

Publication Date

Submission Date

Acceptance Date

Published in Issue

DOI

IZ

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