Sains Malaysiana 38(6)(2009): 939–945

Identification of Immune-related Genes by Analysis of

Spleen Expressed Sequence Tags from the Asian Seabass, Lates calcarifer

(Pengenalpastian Gen Berkaitan Imun melalui Analisis Penanda Jujukan Terungkap Limpa

daripada Ikan Siakap, Lates calcarifer)

Nurul-Yuziana Mohd-Yusof, Chee-Choong Hoh, Adura Mohd-Adnan & Kiew-Lian Wan*

School of Biosciences and Biotechnology

Faculty of Science and Technology, Universiti Kebangsaan Malaysia

43600 UKM Bangi, Selangor, Malaysia

Malaysian Genome Institute

Heliks Emas Block, UKM-MTDL Technology Centre

Universiti Kebangsaan Malaysia, 43600 Bangi Selangor D.E., Malaysia

Received: 7 January 2009 / Accepted: 8 April 2009

ABSTRACT

The Asian seabass (Lates calcarifer) is one of the most economically important aquaculture fish species in South East Asia. While the biology of the Asian seabass is widely studied, relatively little information is available at the molecular level. This lack of molecular information represents one obstacle to rapid progress in the study of immune responses particularly under aquaculture conditions. In light of this situation, we have undertaken an expressed sequence tag (EST) project on the Asian seabass spleen, the secondary lymphoid organ, for the identification of immune-related genes. A total of 2932 ESTs were generated and grouped into 1063 unique transcripts (UTs), which consisted of 104 consensi and 959 singletons. Of these, 51.3% (545/1063) matched to previously identified genes, while 48.7% (518/1063) showed no match. Of the 545 homologous UTs, 102 (9.6%) can be putatively identified as immune-related genes. The identification of the putative immune-related genes provides a meaningful framework in the effort to comprehend the Asian seabass immune system that may lead to an increase in the understanding of the defense mechanisms of and our abilities to manage this fish species.

Keywords: Fish immune system; innate immunity; transcriptome

ABSTRAK

Ikan siakap (Lates calcarifer) merupakan salah satu daripada spesies ikan akuakultur yang terpenting daripada segi ekonomi di rantau Asia Tenggara. Walaupun biologi ikan siakap banyak dikaji, namun maklumat pada peringkat molekul mengenai biologi spesies ikan ini masih kurang. Kekurangan maklumat molekul ini merupakan salah satu sebab yang menghalang kemajuan dalam kajian gerak balas imun terutamanya dalam sekitaran akuakultur. Memandangkan keadaan ini, kami telah menjalankan projek penanda jujukan terungkap (EST) terhadap limpa ikan siakap, yang merupakan organ limfoid sekunder, bagi mengenalpasti gen berkaitan imun. Sejumlah 2932 EST telah dijana dan dikelompokkan ke dalam 1063 transkrip unik (UT), yang terdiri daripada 104 konsensus dan 959 tunggalan. Daripada jumlah ini, 51.3% (545/1063) mempunyai padanan terhadap gen yang pernah dicirikan, manakala 48.7% (518/1063) tidak menunjukkan sebarang padanan. Di antara 545 UT yang mempunyai homologi, 102 (9.6%) boleh dikenalpasti secara putatif sebagai gen berkaitan imun. Pengenalpastian gen berkaitan imun putatif menyediakan kerangka yang berguna dalam usaha untuk memahami sistem imun ikan siakap yang mungkin dapat membawa kepada peningkatan pemahaman mengenai mekanisme pertahanan dan keupayaan kita untuk mengurus spesies ikan ini.

Kata kunci: Keimunan inat; sistem keimunan ikan; transkriptom

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*Corresponding author; email: klwan@ukm.my