Abstract Detail

Comparative Genomics/Transcriptomics

Jansen, Robert [1], Ruhlman, Tracey [2], Goncalves, Deise [3].

Misconceptions about Plastome Organization and Evolution.

The plant systematics community has been utilizing plastid genomes (plastomes) for phylogenetic and evolutionary studies since the middle 1980s. Most of the early research utilized restriction site comparisons to identify both structural rearrangements and restriction site variation for phylogeny reconstruction. The advent of next generation sequencing made it possible to accumulate large quantities of sequence reads that could be used to assemble complete or nearly complete plastomes. This resulted in an explosive increase in the availability of plastome sequences across land plants with over 3000 annotated plastomes currently available on GenBank. During the same time period, plant molecular biologists greatly enhanced the understanding of the structure, repair, replication, recombination, transcription and translation of plastid DNA. Unfortunately most plant systematists are either unaware or have ignored this knowledge, which has resulted in misrepresentation of several phenomena that are critical for phylogenetic and evolutionary studies using the plastome. We believe that it is time to stop perpetuating misconceptions about plastome organization and evolution. The five main misconceptions are: (1) plastomes are circular and the multiple copies present in plastids are identical; (2) recombination between copies of the inverted repeat (IR) occurs between IRs on the same circular genome by flip-flop recombination; (3) recombination occurs exclusively between repeated sequences within a unit genome to generate inversions; (4) detection of a transcription product is evidence that a plastid-encoded gene is functional; and (5) plastid genes are fully linked, therefore it is appropriate to concatenate all genes in phylogenetic analyses. These misconceptions can lead to inaccurate phylogenies, incorrect models of plastome structural evolution and false reports of gene presence/absence. Thus, we strongly encourage the plant systematics community to incorporate information about plastome molecular biology when using this genome for phylogenetic and evolutionary investigations.

1 - University Of Texas At Austin, Integrative Biology, 205 W. 24th St. Stop C0930, Austin, TX, 78712, United States
2 - University of Texas at Austin, Integrative Biology, 205 W. 24th St. Stop C0930, TX, 78712, USA
3 - University of Texas at Austin, Integrative Biology, 205 W. 24th St. Stop C0930, Austin, TX, 78712, USA

Keywords:
plastome
recombination
transcription
phylogenomics.

Presentation Type: Poster
Session: P, Comparative Genomics and Transcriptomics Posters
Location: /
Date: Monday, July 29th, 2019
Time: 5:30 PM This poster will be presented at 5:30 pm. The Poster Session runs from 5:30 pm to 7:00 pm. Posters with odd poster numbers are presented at 5:30 pm, and posters with even poster numbers are presented at 6:15 pm.
Number: PGT009
Abstract ID:417
Candidate for Awards:None