Assembly and analysis of variability of organelle genomes in common ragweed (Ambrosia artemisiifolia)

Terzer, Vid (author), Gostinčar, Cene (mentor), Hodgins, Kathryn (comentor)

Invasive species pose significant threats to biodiversity, agriculture, and human health, with impacts intensified by climate change. They also provide a unique opportunity to study rapid evolutionary processes. Ambrosia artemisiifolia, a highly invasive weed from North America, has caused substantial environmental and health impacts worldwide. This study assembled and annotated the chloroplast (152,471 bp) and mitochondrial (283,153 bp) genomes of A. artemisiifolia using short sequencing reads, providing a new reference for examining its genetic diversity and evolutionary history. Annotation revealed 80 protein-coding genes, 36 tRNAs, and 4 rRNAs in the chloroplast and 40 protein-coding genes, 21 tRNAs, and 5 rRNAs in the mitochondrion. Analyses of samples from North America, Europe, and Australia using principal component analysis, maximum likelihood phylogenies, and minimum spanning networks identified distinct genetic clusters, with clear geographic structure in North America and reduced structuring in Europe and Australia. The highest organelle genome variability was in the North American range and Europe, while the lowest was in Australia. Phylogenetic analyses revealed signs of organelle-specific introgression with close relatives. Differences in chloroplast and mitochondrial structuring highlighted independent inheritance and evolutionary history. This study provides valuable insights into the global spread and adaptation of A. artemisiifolia, enhancing understanding of its invasion history and evolutionary dynamics.

• Language: English
• Keywords: Ambrosia artemisiifolia L., invasive species, chloroplast, mitochondria, genomics, genome assembly, annotation, PCA, phylogenetic trees, minimum spanning networks, geographical structuring of populations, genome variability
• Work type: Master's thesis/paper
• Typology: 2.09 - Master's Thesis
• Organization: BF - Biotechnical Faculty
• Publisher: [V. Terzer]
• Year: 2025
• PID: 20.500.12556/RUL-167587
• UDC: 575.111:574.9(043.2)
• COBISS.SI-ID: 227765507
• Publication date in RUL: 01.03.2025

Secondary language

• Language: Slovenian
• Title: Sestavljanje in analiza variabilnosti genomov organelov pelinolistne žvrklje (Ambrosia artemisiifolia)

Abstract

Invazivne vrste predstavljajo pomembno grožnjo biotski raznovrstnosti, kmetijskim dejavnostim in zdravju ljudi, njihov vpliv pa dodatno povečujejo podnebne spremembe. Obenem invazivke ponujajo tudi edinstveno priložnost za preučevanje hitrih evolucijskih procesov. Ambrosia artemisiifolia je izredno invazivna plevelna vrsta iz Severne Amerike. Povzroča negativne okoljske in zdravstvene vplive po vsem svetu. V tej nalogi smo z uporabo kratkih odčitkov sestavili in anotirali genom kloroplasta (152.471 bp) in mitohondrija (283.153 bp) te rastline in s tem pripravili osnovo za preučevanje njene genetske raznovrstnosti in evolucijske zgodovine. Anotacija je razkrila 80 protein-kodirajočih genov, 36 tRNA in 4 rRNA v kloroplastu ter 40 protein-kodirajočih genov, 21 tRNA in 5 rRNA v mitohondriju. Analize vzorcev iz Severne Amerike, Evrope in Avstralije z uporabo analize glavnih komponent, filogenetskih dreves z metodo največjega verjetja in minimalnih raztezajočih se omrežij smo identificirali ločene genetske skupine, pri čemer je bila v Severni Ameriki zaznana jasna geografska struktura, v Evropi in Avstraliji pa zmanjšana. Največjo variabilnost organelnih genomov smo zaznali v Severni Ameriki in Evropi, najnižjo pa v Avstraliji. Filogenetske analize so razkrile znake hibridizacije organelov s sorodnimi vrstami. Razlike v strukturiranju kloroplastov in mitohondrijev poudarjajo njuno neodvisno dedovanje in evolucijsko zgodovino. Magistrsko delo ponuja nov vpogled v proces globalnega širjenja in prilagoditev A. artemisiifolia ter prispeva k razumevanju zgodovine njene invazije in evolucije.

• Keywords: Ambrosia artemisiifolia L., invazivne vrste, kloroplast, mitohondrij, genomika, sestavljanje genoma, anotacija, PCA, filogenetska drevesa, analiza omrežij, geografska struktura populacij, variabilnost genoma