Tam Tetragenococcus genomlarında karşılaştırmalı genomik: Profajlar, ıs elemanları ve savunma sistemleri

Öz

Tetragenococcus türleri, bakteriyofajlar ve mobil DNA’nın suş stabilitesi ve performansını etkileyebileceği yüksek tuzlu fermentasyonlarda önemli laktik asit bakterileridir. Ancak tamamlanmış genom sayısı sınırlıdır ve bu durum soy yapısının ve mobil/savunma mimarisinin sağlam biçimde çıkarımını kısıtlamaktadır. Bu çalışma in silico olarak yürütülmüştür. Bu çalışmada RefSeq’den seçilen 11 tamamlanmış genom (dokuz Tetragenococcus halophilus ile T. koreensis ve T. osmophilus) kıyaslamalı genomik yöntemlerle analiz edilmiştir. Çekirdek genom filojenisi ve ortalama nükleotid benzerliği (ANI) sonuçları, mobil ve savunma özelliklerinin yorumlanması için mevcut tamamlanmış genom seti içinde bir soy iskeleti sağlamıştır. İnsersiyon dizileri (IS), genomların tamamında saptanmış ancak suşlar arasında belirgin değişkenlik göstermiştir; buna karşılık profaj sinyali genomların bir kısmında yoğunlaşmıştır. Bu bulgular, transpozisyon ilişkili yük ile öngörülen profaj taşınmasının suşlar arasında eşit olmayan katkılar gösterebildiğini düşündürmektedir. Savunma repertuarları heterojen bulunmuş ve kompakt genomlarda dahi CRISPR dışı birden fazla savunma sistemi görülmüştür. CRISPR spacer dizileri, veri seti içindeki profaj kaynaklı dizilerle yapısal ve uniform olmayan bir biçimde eşleşmiş; bu durum, ilişkili mobil elementlere maruziyetin soy geçmişleriyle uyumlu bulunmuştur. Tamamlanmış genom örnekleminin küçük olması ve bulguların biyoinformatik öngörülere dayanması, calışmanın kısıtıdır. Sonuç olarak, bu çalışma Tetragenococcus’ta mobilom bileşimi ile savunma potansiyelini soy düzeyinde ilişkilendiren bir çerçeve sunmakta ve yüksek tuzlu fermentasyonlarda faj-konak etkileşimlerine ilişkin takip çalışmalarını desteklemektedir.

Anahtar Kelimeler

• Tetragenococcus
• Fermentasyon mikrobiyolojisi
• Mobil genetik element
• CRISPR-Cas
• Bakteriyel savunma sistemleri
• Profajlar

Comparative genomics of complete Tetragenococcus genomes: Prophages, is elements, and defense systems

Öz

Tetragenococcus species are key lactic acid bacteria in high-salt fermentations, where bacteriophages and mobile DNA may influence strain stability and performance. Complete genomes remain limited, which constrains robust inference of lineage structure and mobile/defense architecture. This study was conducted in silico. In this study, 11 RefSeq complete genomes (nine Tetragenococcus halophilus plus T. koreensis and T. osmophilus) were analyzed using a comparative genomics workflow integrating core genome phylogeny and average nucleotide identity (ANI) with computational prediction of prophages, insertion sequences, CRISPR-Cas loci, and additional defense systems. Marked lineage structure was resolved, providing a scaffold for interpreting mobile and defense features within the available complete genome set. Insertion sequence elements were detected broadly but varied substantially among strains, whereas prophage signal was concentrated in a subset of genomes, indicating non-uniform contributions of transposition and prophage carriage across lineages. Defense repertoires were heterogeneous, with multiple non-CRISPR systems predicted even in compact genomes. CRISPR spacers aligned to within-dataset prophage-derived sequences in a structured, non-uniform pattern, consistent with lineage-specific histories of exposure to related mobile elements. Key limitations included small complete genome sampling and reliance on computational predictions. Overall, these complete-genome comparisons establish a lineage-resolved framework for describing mobilome and defense variation in Tetragenococcus and support follow-up work relevant to phage host interactions in high-salt fermentations.

Anahtar Kelimeler

• Tetragenococcus
• Fermentation microbiology
• Mobile genetic element
• CRISPR-Cas
• Bacterial defense systems
• Prophages

Kaynakça

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