Abstract Detail

Comparative Genomics/Transcriptomics

Shrestha, Bikash [1], Weng, Mao-Lun [2], Theriot, Edward [1], Gilbert, Lawerence [1], Ruhlman, Tracey [1], Krosnick, Shawn [3], Jansen, Robert [1].

Highly accelerated rates of genomic rearrangements and nucleotide substitutions in plastid genomes of Passiflora subgenus Decaloba.

Plastid genomes (plastomes) of photosynthetic angiosperms are for the most part highly conserved in their organization, mode of inheritance and rates of nucleotide substitution. A small number of distantly related lineages share a syndrome of features that deviate from this general pattern, including extensive genomic rearrangements, accelerated rates of nucleotide substitution, biparental inheritance and plastome-genome incompatibility. Previous studies of plastomes in Passiflora with limited taxon sampling suggested that the genus exhibits this syndrome. To examine this phenomenon further, 15 new plastomes from Passiflora were sequenced and combined with previously published data to examine the phylogenetic relationships, genome organization and evolutionary rates across all five subgenera and the sister genus Adenia. Phylogenomic analyses using 68 shared protein-coding genes generated a fully resolved and strongly supported tree that is congruent with previous phylogenies based on a few plastid and nuclear loci. This phylogeny was used to examine the distribution of plastome rearrangements across Passiflora. Multiple gene and intron losses and inversions were identified in Passiflora with some occurring in parallel and others that extended across the Passifloraceae. Furthermore, extensive expansions and contractions of the inverted repeat (IR) were uncovered and in some cases this resulted in exclusion of all ribosomal RNA genes from the IR. The most highly rearranged lineage was subgenus Decaloba, which experienced extensive IR expansion that incorporated up to 25 protein-coding genes usually located in large single copy region. Nucleotide substitution rate analyses of 68 protein-coding genes across the genus showed locus- and lineage-specific acceleration. Significant increase in dS, dN and dN/dS was detected for clpP across the genus and for ycf4 in certain lineages. Significant increases in dN and dN/dS for ribosomal subunits and RNA polymerase genes were detected in the branch leading to the expanded IR-clade in subgenus Decaloba. This subgenus displays the syndrome of unusual features, making it an ideal system to investigate the dynamic evolution of angiosperm plastomes.

1 - The University of Texas at Austin, Integrative Biology, 2415 Speedway #C0930, Austin, Texas, 78712, USA
2 - Westfield State University, Department of Biology, 577 Western Avenue, Westfield, MA, 01086, USA
3 - Tennessee Tech University, Dept. Of Biology, 1100 North Dixie Avenue, Pennebaker Hall #207, Cookeville, TN, 38505, United States

Keywords:
Passifloraceae
IR expansion/contraction
plastid-encoded RNA polymerase
inversion
substitution rate analyses.

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: PGT005
Abstract ID:343
Candidate for Awards:Genetics Section Poster Award