Abstract Detail

Seed-free Plants at the Genomic Scale

Satjarak, Anchittha [1], Graham, Linda E. [1].

Comparative studies of prasinophyte chloroplast genomes.

Prasinophytes form a paraphyletic assemblage of early diverging green algae. The heterogeneity in their morphologies and the results of phylogenetic analyses of some marker genes suggest that prasinophytes have the potential to reveal the traits of the last common ancestor of the main two green lineages: 1) chlorophyte algae, the putative clade that includes the majority of the modern green algal species, and 2) streptophyte algae, a smaller paraphyletic assemblage known to be closely related to land plants. Therefore, understanding the genetic composition of prasinophyte algae is fundamental to understanding the diversification and evolutionary process that may have occurred in both green lineages. In this study, we report the newly sequenced chloroplast genome of Pyramimonas parkeae NIES254 and comparative studies at the inter-specific level and intra-specific level of prasinophyte chloroplast genomes. The results showed that, at both levels, prasinophyte chloroplast genomes show high variability in their organization, gene content, and gene order. It is also worth noting that the differences we observed at the intra-specific level of P. parkeae is currently the highest variability known to occur at the intra-specific level. The variability has 5 aspects. First, the genome size of NIES254 and another strain (CCMP726) are not the same. NIES254 chloroplast genome is longer than that of CCMP726 by 3,024 bp and the variation in length is present in all three informative regions: LSC (288 bp), SCC (5,088 bp), and IR (1,086 bp). Second, there are four large hotspot regions where the similarity value between the two studied strains is close to zero. Third, this is the first evidence of inverted repeat boundary movement at the intra-specific level. Fourth, the boundaries of the inverted repeat at the IR-SSC junction have undergone contraction or expansion not for just a few nucleotides, but for about 2.5 kbp, resulting in differences in copy number of three protein coding genes: ycf20, psaC, and ndhE. Fifth, protein coding genes present in the chloroplast genomes have been subjected to different selection pressure, judged by uneven substitution rate. Most genes were subjected to purifying selection but atpH, petA, petN, psaJ, psbI, psbK, psbL, psbZ, and ycf12 exhibit neutral mutation.

1 - University of Wisconsin-Madison, Botany, 430 Lincoln Drive, Madison , WI, 53706, USA

Keywords:
none specified

Presentation Type: Colloquium Presentations
Session: C4, Seed Free Plants at the Genomic Scale
Location: Chatham Ballroom - C/Savannah International Trade and Convention Center
Date: Wednesday, August 3rd, 2016
Time: 2:15 PM
Number: C4004
Abstract ID:232
Candidate for Awards:None