Extracting “legacy” genes from an invertebrate sequence capture dataset to complement phylogenomic datasets

Caroline Miller

Authors:  Caroline Miller, Michael Forthman, Rebecca T. Kimball, Christine W. Miller

Faculty Mentor: Dr. Michael Forthman

College:  College of Agricultural and Life Sciences


The field of phylogenetics has greatly benefited from the introduction of next-generation sequencing (NGS) and genome reduction approaches, allowing molecular datasets to consist of thousands of loci from model and non-model species. These phylogenetic studies result in rich datasets comprised of targeted regions of the genome but can also include off-target reads. Molecular datasets comprised of loci from NGS genome reduction approaches are superseding Sanger-based datasets that target a few well-known loci (“legacy markers”). However, integrating these types of datasets is of interest as legacy markers can include different types of loci (e.g., mitochondrial, ribosomal, and nuclear protein coding) across a potentially larger sample of species from past phylogenetic studies. Here, I am using existing legacy data for a group of leaf-footed bugs (Hemiptera: Coreoidea) — a model group for sexual selection studies — to recover legacy markers from off-target sequences in an existing NGS genome reduced dataset comprised of protein-coding ultraconserved elements. Specifically, I use two bioinformatic resources to extract legacy markers from off-target sequences: (1) MitoFinder to retrieve mitochondrial loci (2) and BLAST to retrieve nuclear protein coding and ribosomal loci.

Poster Pitch

Click the video below to view the student's poster pitch.


Click the image to enlarge.
20 Responses
    1. Caroline Miller

      Dear Dr. Miller,

      Thank you so much for your comment, I appreciate it! I am so lucky to be a part of this incredible lab!

  1. Dr Ginny Greenway

    Nice poster Caroline! Great to see how new techniques are helping to get the most information possible out of existing genomic datasets.

    1. Caroline Miller

      Dear Ginny,

      Thank you so much, I appreciate it! Yes, I agree new techniques and publically available resources are facilitating some great and interesting research.

    1. Caroline Miller

      Dear Hadley,

      Thank you so much, I appreciate it! I found it really interesting that we could accomplish what the study aimed to do and successfully extract some legacy data from an existing sequence capture dataset. I think that this highlights how we can accomplish some great and interesting research without expending costs for baits to target specific loci, (i.e., mitochondrial and nuclear), when we may already have this data generated!

    1. Caroline Miller

      Dear Michael,

      This could NOT have all come together without you! Thank you SO much for everything!

  2. Jimmy Peniston

    Great presentation and poster! You did a great job explaining some complicated concepts in a very understandable way. I definitely learned a lot. Thank you!

    1. Caroline Miller

      Dear Jimmy,

      Thank you so much, I really appreciate it! One of the most difficult parts of preparing this presentation was finding a way to relay this information in a clear, concise, and graphic manner that could be understood by the general public. I am so glad that the concepts came across as understandable!

  3. Sara Zlotnik

    Hi Caroline,

    Great job on making a very visually appealing and super informative poster! You also explained the technical aspects of your methods really clearly. Thanks for sharing your awesome research with everyone!


    1. Caroline Miller

      Dear Sara,

      Thank you so much, I appreciate it! I am glad that the methods flowed so that it was easy to follow. I certainly worked/designed my presentation so that I presented the methods in a parallel manner to make sure it is understandable/more understandable. Thank you for your support!

  4. Caroline Miller

    Dear Dr. Wysocki,

    Thank you so much, I appreciate it! I am so glad the presentation translated!