Phylogenomics

Phylogenomics involves the reconstruction of evolutionary relationships by comparing sequences of whole genomes or portions of genomes.

Latest Research and Reviews

  • Research | | open

    A high-quality reference genome of the stout camphor tree reveals its genome evolution and supports that magnoliid and eudicot lineages share more common ancestry relative to monocots.

    • Shu-Miaw Chaw
    • , Yu-Ching Liu
    • , Yu-Wei Wu
    • , Han-Yu Wang
    • , Chan-Yi Ivy Lin
    • , Chung-Shien Wu
    • , Huei-Mien Ke
    • , Lo-Yu Chang
    • , Chih-Yao Hsu
    • , Hui-Ting Yang
    • , Edi Sudianto
    • , Min-Hung Hsu
    • , Kun-Pin Wu
    • , Ling-Ni Wang
    • , James H. Leebens-Mack
    •  & Isheng J. Tsai
    Nature Plants 5, 63-73
  • Research | | open

    Sweetpotato is an important food security crop providing rich source of macro- and micronutrients including carbohydrates and vitamins. Here, the authors assemble of the two diploid relatives of cultivated sweetpotato and identify genes and alleles associated with carotenoid biosynthesis from breeding lines.

    • Shan Wu
    • , Kin H. Lau
    • , Qinghe Cao
    • , John P. Hamilton
    • , Honghe Sun
    • , Chenxi Zhou
    • , Lauren Eserman
    • , Dorcus C. Gemenet
    • , Bode A. Olukolu
    • , Haiyan Wang
    • , Emily Crisovan
    • , Grant T. Godden
    • , Chen Jiao
    • , Xin Wang
    • , Mercy Kitavi
    • , Norma Manrique-Carpintero
    • , Brieanne Vaillancourt
    • , Krystle Wiegert-Rininger
    • , Xinsun Yang
    • , Kan Bao
    • , Jennifer Schaff
    • , Jan Kreuze
    • , Wolfgang Gruneberg
    • , Awais Khan
    • , Marc Ghislain
    • , Daifu Ma
    • , Jiming Jiang
    • , Robert O. M. Mwanga
    • , Jim Leebens-Mack
    • , Lachlan J. M. Coin
    • , G. Craig Yencho
    • , C. Robin Buell
    •  & Zhangjun Fei
  • Research | | open

    Gene synthesis has expanded the ability to modify and create DNA sequences, with implications for biosurveillance. The authors use machine learning and codon theory to identify synthetic genes in Addgene data, and show that synthesis accelerates human-directed gene transfer across the tree of life.

    • Aditya M. Kunjapur
    • , Philipp Pfingstag
    •  & Neil C. Thompson
  • Reviews |

    The virulence of viruses is a major determinant of the health burden of viral infections in humans and other species. In this article, Geoghegan and Holmes discuss how largely disparate research fields — theoretical modelling of virulence evolution and experimental dissection of genetic virulence determinants in laboratory model systems — can be bridged by considering real genomic data of viral evolution in a phylogenetic context. They describe the underlying principles of virulence evolution and how they apply to real-world viral infections and outbreaks of global importance.

    • Jemma L. Geoghegan
    •  & Edward C. Holmes

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