CHLOROPLAST GENOME SEQUENCING IN BRASSICACEAE AND ITS PHYLOGENETIC APPLICATIONS: A COMPREHENSIVE REVIEW

Abstract

The Brassicaceae family is important both scientifically and economically; however, its complex evolutionary history, characterized by rapid diversification, whole-genome duplications, and significant reticular evolution, makes its classification challenging. The advent of high-throughput next-generation sequencing technology has facilitated the shift from single-locus phylogenomics to whole-plastome phylogenomics, improving our understanding of the family's deep evolutionary relationships. This comprehensive review reinforces our understanding of Brassicaceae chloroplast genomes, highlighting the highly consistent gene content, distinctive base composition patterns, and highly conserved quadruple structure. Phylogenetically relevant structural changes, including temporal shifts in the boundaries of inverted repeats (IRs), lineage-specific gene losses (e.g., rps16), and the loss of ndh genes in response to local adaptive pressures, are investigated in this study. Furthermore, the effectiveness of plastid phylogenics in clarifying taxonomically complex clades was evaluated, while directly addressing common problems such as cytonuclear incompatibility, chloroplast capture, and soft polytomies at key backbone nodes. The article examined newly developed methodologies, including genome scanning, advanced assembly tools such as GetOrganelle, and multispecies merger phylogenetic reconstruction. Finally, potential future developments were discussed, highlighting the necessity of multi-genome integration, the application of pan-plastome methodologies, and the expanding possibilities of chloroplast synthetic biology and genome editing to improve agriculture.

Keywords

• Brassicaceae
• chloroplast genome
• plastomics
• phylogenomics
• genome skimming

BRASSICACEAE'DE KLOROPLAST GENOM DİZİLEMESİ VE FİLOGENETİK UYGULAMALARI: KAPSAMLI BİR İNCELEME

Abstract

Brassicaceae familyası hem bilimsel hem de ekonomik açıdan önemlidir; ancak hızlı çeşitlenmeler, tüm genom duplikasyonları ve önemli ağsı evrimle karakterize edilen karmaşık evrimsel tarihi, sınıflandırmasını zorlaştırmaktadır. Yüksek verimli yeni nesil dizileme teknolojisinin ortaya çıkışı, tek lokuslu filogenomikten tüm plastom filogenomikine geçişi kolaylaştırarak, familyanın derin evrimsel ilişkilerine dair anlayışımızı geliştirmiştir. Bu kapsamlı inceleme, Brassicaceae kloroplast genomlarına dair anlayışımızı pekiştirmektedir. Gen içeriklerinin son derece tutarlılığına, ayırt edici baz bileşim kalıplarına ve oldukça korunmuş dörtlü yapısına vurgu yapmaktadır. Ters tekrarların (IR'ler) sınırlarında zamansal değişiklikler, soy hattına özgü gen kayıpları (örneğin rps16) ve yerel adaptif baskılara yanıt olarak ndh genlerinin kaybı da dahil olmak üzere, filogenetikle ilgili yapısal değişiklikler bu çalışmada incelenmiştir. Ayrıca, sitonükleer uyumsuzluk, kloroplast yakalama ve önemli omurga düğümlerindeki yumuşak politomiler gibi yaygın sorunları doğrudan ele alırken, taksonomik olarak karmaşık kladların açıklığa kavuşturulmasında plastid filogenomiğinin etkinliği değerlendirilmiştir. Makale, genom taraması, GetOrganelle gibi gelişmiş montaj araçları ve çok türlü birleşme filogenetik rekonstrüksiyonu da dahil olmak üzere yeni geliştirilen metodolojileri incelemiştir. Son olarak, çoklu genom entegrasyonunun gerekliliğini, pan-plastom metodolojilerinin uygulanmasını ve tarımı geliştirmek için kloroplast sentetik biyolojisi ve genom düzenlemesinin genişleyen olanaklarını vurgulayarak potansiyel gelecekteki gelişmeler tartışılmıştır.

Keywords

• Brassicaceae
• kloroplast genomu
• plastomik
• filogenomik
• genom taraması

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