Peng SUN, Yong FU, Qiaofeng WAN, Mohamed YOSRI, Shenghu HE, Xiuying SHEN

Complete Genome Sequencing of Mycoplasma bovis Type Strain Ningxia-1 and Systematic Bioinformatic Characterization for Housekeeping-related Genes

Mycoplasma bovis is a major pathogen leading to bovine respiratory disease syndrome. The worldwide prevalence of this pathogen has caused enormous economic losses in the beef industry. Substantial efforts have been made to identify and characterize the surface proteins of M. bovis. However, little is known regarding experimentally proved housekeeping genes, or the distribution and the number of motifs within these genes in M. bovis. We used Picbio SMRT technology of next-generation sequencing for M. bovis Ningxia-1 isolation and applied different tools (Mega X, STRING v11.0, TMHMM v2.0, MOTIF) for bioinformatics analysis. The present study compared M. bovis Ningxia-1 strain with another ten M. bovis strains with sequenced whole genome and identified 24 housekeeping genes in each strain. The phylogenetic tree indicates a close relationship between M. bovis Ningxia-1 with NM2012 based on BLAST results of these genes. Within the 24 housekeeping genes in M. bovis Ningxia-1 stain, 3/24 (12.5%) of the genes have the potential to be used as internal control genes, 2 sets of proteins have interactions which have been proved under experimental and database conditions. MetG is a putative transmembrane protein, while others are predicted to be located outside of the membrane. Additionally, there are 6 common motifs distributed among 7 of the proteins (29.17%). Our bioinformatic analysis is intended to provide new and complementary data in mining and making comparisons of housekeeping genes through M. bovis type strain Ningxia-1 sequencing.

Mycoplasma bovis Ningxia-1 Suşunun Tüm Genom Sekanslaması ve Housekeeping İlişkili Genlerin Sistematik Biyoinformatik Karakterizasyonu

Mycoplasma bovis, sığır solunum hastalığı sendromuna yol açan önemli bir patojendir. Bu patojenin dünya çapında yaygınlığı, sığır eti endüstrisinde büyük ekonomik kayıplara neden olmuştur. M. bovis’in yüzey proteinlerini tanımlamak ve karakterize etmek için önemli çabalar sarf edilmiştir. Bununla birlikte, M. bovis‘te deneysel olarak kanıtlanmış housekeeping genleri veya bu genler içindeki motiflerin dağılımı ve sayısı hakkında çok az şey bilinmektedir. M. bovis Ningxia-1 izolasyonu için yeni nesil sekanslama Picbio SMRT teknolojisini kullandık ve biyoinformatik analiz için farklı araçlar (Mega X, STRING v11.0, TMHMM v2.0, MOTIF) uyguladık. Bu çalışma ile M. bovis Ningxia-1 suşu, sekanslanmış tam genomlu başka bir M. bovis suşu ile karşılaştırıldı ve her suşta 24 housekeeping geni tanımladı. Filogenetik ağaç, bu genlerin BLAST sonuçlarına dayanarak M. bovis Ningxia-1 ile NM2012 arasında yakın bir ilişki olduğunu gösterdi. M. bovis Ningxia-1 boyasındaki 24 housekeeping geni içinde, genlerin 3/24’ü (%12.5) internal kontrol genleri olarak kullanılma potansiyeline sahiptir, proteinlerin 2 seti deneysel ve veritabanı koşullarında kanıtlanmış etkileşim göstermektedir. MetG varsayılan bir transmembran protein olmasına rağmen, diğerlerinin membranın dışında olduğu tahmin edilmektedir. Ek olarak, 7 proteine (%29.17) dağılmış 6 yaygın motif bulunmaktadır. Biyoinformatik analizimiz, veri madenciliğinde yeni ve tamamlayıcı veriler ortaya koymuş ve M. bovis tipi Ningxia-1 dizileme yoluyla temel genlerin karşılaştırmalarını yapmayı sağlamıştır.

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