Abstract Detail

Genomics / Proteomics

Barrett, Craig [1], Freudenstein, John [2], Li, Jeff [3], Lim, Gwynne [4], Mayfield-Jones, Dustin [5], Perez, Leticia [6], Pires, J. Chris [7], Davis, Jerrold [8].

Investigating the process of plastome degradation in an early-transitional mycoheterotrophic genus, Corallorhiza (Orchidaceae).

Parasites frequently display patterns of extreme reduction in morphological and genomic features.  One example is that of parasitic angiosperms, including holoparasites and obligate mycoheterotrophs.  Plastome evolution in these plants is of particular interest, because selective constraints of photosynthetic function are presumably relaxed, allowing loss-of-function mutations to accumulate, at least for genes involved in photosynthesis.  Recent studies have documented cases of extreme reduction and degradation in parasitic plastomes (e.g., Orobanchaceae; Rhizanthella), and perhaps even loss of the plastome (Rafflesia).  Fewer studies have focused on earlier stages of the transition from autotrophy to heterotrophy.  Corallo­rhiza is a genus that exemplifies this transition, in that it contains partially mycoheterotrophic species—that retain photosynthetic function—and fully mycoheterotrophic species that have presumably lost photosynthesis.  How does the process of plastome degradation proceed in such a group of closely related organisms?  Is there a logical order of pseudogene formation/gene loss among the various plastid-encoded gene systems?  To address these questions, genomic DNA was sequenced for 11 members of Corallorhiza on an Illumina HiSeq 2000 to generate 100 bp paired-end reads.  Reads were quality-trimmed and assembled de novo, resulting in complete, annotated plastomes.  Plastome sizes within the genus ranged from 137,505 bp (C. striata vreelandii) to 151,030 bp (C. macrantha); plastomes of putatively non-photosynthetic taxa (C. striata vreelandii, C. maculata complex) were on average ~3 kb shorter than those of putatively photosynthetic taxa (e.g., C. trifida, C. macrantha, C. odontorhiza).  Phylogenetic analysis yielded a highly resolved and supported plastid tree, especially among members of the previously unresolved C. maculata complex.  All green taxa had completely intact reading frames for all major gene systems except ndh.  Plastomes of non-green species, however, displayed evidence of pseudogenization/loss, representing at least two independent degradation pathways in the genus.  Interestingly, no species showed evidence of pseudogenes for the ATP-synthase complex.  Corallorhiza striata displayed the most degraded plastome, with nearly all photosynthesis-related genes showing some evidence for loss-of-function.  The C. maculata complex showed a gradual transition to loss-of-function, including a 16 kb inversion in the LSC region of var. maculata.  These data represent an empirical test of a previously proposed general model of plastome degradation (Barrett and Davis, 2012), and demonstrate that Corallorhiza is a valuable system for understanding genomic and morphological consequences of parasitism from a non-animal perspective, potentially providing clues to the roles of plastids outside of photosynthesis in future studies.

1 - California State University, Los Angeles, Department of Biological Sciences, 214 LaKretz Hall, 5151 State University Dr, Los Angeles, CA, 90032, USA
2 - Ohio State University, Dept. of Evolution, Ecology, and Organismal Biology; OSU Museum of Biological Diversity, 1315 Kinnear Rd, Columbus, OH, 43212, USA
3 - California State University, Los Angeles, Biological Sciences
4 - Cornell University/New York Botanical Garden, Plant Biology
5 - University of Missouri - Columbia, Division of Biological Sciences
6 - California State University, Los Angeles
7 - University Of Missouri, 371 Bond Life Sciences Center, 1201 Rollins Street, Columbia, MO, 65211-7310, USA
8 - Cornell University, Department of Plant Biology, 512 Mann Library, Ithaca, NY, 14850, USA

Keywords:
parasitic
chloroplast
Photosynthesis
pseudogene
deletion
coralroot
orchid
fungus.

Presentation Type: Oral Paper:Papers for Topics
Session: 35
Location: Pines South/Boise Centre
Date: Wednesday, July 30th, 2014
Time: 11:15 AM
Number: 35013
Abstract ID:219
Candidate for Awards:None