The University of Southampton
University of Southampton Institutional Repository

Evolution of red algal plastid genomes: ancient architectures, introns, horizontal gene transfer, and taxonomic utility of plastid markers

Evolution of red algal plastid genomes: ancient architectures, introns, horizontal gene transfer, and taxonomic utility of plastid markers
Evolution of red algal plastid genomes: ancient architectures, introns, horizontal gene transfer, and taxonomic utility of plastid markers
Red algae have the most gene-rich plastid genomes known, but despite their evolutionary importance these genomes remain poorly sampled. Here we characterize three complete and one partial plastid genome from a diverse range of florideophytes. By unifying annotations across all available red algal plastid genomes we show they all share a highly compact and slowly-evolving architecture and uniquely rich gene complements. Both chromosome structure and gene content have changed very little during red algal diversification, and suggest that plastid-to nucleus gene transfers have been rare. Despite their ancient character, however, the red algal plastids also contain several unprecedented features, including a group II intron in a tRNA-Met gene that encodes the first example of red algal plastid intron maturase – a feature uniquely shared among florideophytes. We also identify a rare case of a horizontally-acquired proteobacterial operon, and propose this operon may have been recruited for plastid function and potentially replaced a nucleus-encoded plastid-targeted paralogue. Plastid genome phylogenies yield a fully resolved tree and suggest that plastid DNA is a useful tool for resolving red algal relationships. Lastly, we estimate the evolutionary rates among more than 200 plastid genes, and assess their usefulness for species and subspecies taxonomy by comparison to well-established barcoding markers such as cox1 and rbcL. Overall, these data demonstrates that red algal plastid genomes are easily obtainable using high-throughput sequencing of total genomic DNA, interesting from evolutionary perspectives, and promising in resolving red algal relationships at evolutionarily-deep and species/subspecies levels.
1932-6203
Janouskovec, Jan
fbaa4a5d-872e-465b-b2c3-bb35df455cc6
Liu, Shao-Lun
59a34934-3070-47dc-aa32-3e00015dfbd6
Martone, Patrick T.
b4fda6cb-540f-41a1-b7b5-4fb5ff4eba9a
Carre, Wilfrid
d58cde73-a8da-40ab-bdc4-2e7eb8744576
Leblanc, Catherine
28de821c-4deb-4e20-a019-af0c3cfbce1f
Collen, Jonas
5d0b5f39-ea39-4ff2-bd18-a39947b9e86c
Keeling, Patrick J.
fd51c2ef-1daa-442d-b186-71001aa7ca7d
Janouskovec, Jan
fbaa4a5d-872e-465b-b2c3-bb35df455cc6
Liu, Shao-Lun
59a34934-3070-47dc-aa32-3e00015dfbd6
Martone, Patrick T.
b4fda6cb-540f-41a1-b7b5-4fb5ff4eba9a
Carre, Wilfrid
d58cde73-a8da-40ab-bdc4-2e7eb8744576
Leblanc, Catherine
28de821c-4deb-4e20-a019-af0c3cfbce1f
Collen, Jonas
5d0b5f39-ea39-4ff2-bd18-a39947b9e86c
Keeling, Patrick J.
fd51c2ef-1daa-442d-b186-71001aa7ca7d

Janouskovec, Jan, Liu, Shao-Lun, Martone, Patrick T., Carre, Wilfrid, Leblanc, Catherine, Collen, Jonas and Keeling, Patrick J. (2013) Evolution of red algal plastid genomes: ancient architectures, introns, horizontal gene transfer, and taxonomic utility of plastid markers. PLoS ONE, 8 (3). (doi:10.1371/JOURNAL.PONE.0059001).

Record type: Article

Abstract

Red algae have the most gene-rich plastid genomes known, but despite their evolutionary importance these genomes remain poorly sampled. Here we characterize three complete and one partial plastid genome from a diverse range of florideophytes. By unifying annotations across all available red algal plastid genomes we show they all share a highly compact and slowly-evolving architecture and uniquely rich gene complements. Both chromosome structure and gene content have changed very little during red algal diversification, and suggest that plastid-to nucleus gene transfers have been rare. Despite their ancient character, however, the red algal plastids also contain several unprecedented features, including a group II intron in a tRNA-Met gene that encodes the first example of red algal plastid intron maturase – a feature uniquely shared among florideophytes. We also identify a rare case of a horizontally-acquired proteobacterial operon, and propose this operon may have been recruited for plastid function and potentially replaced a nucleus-encoded plastid-targeted paralogue. Plastid genome phylogenies yield a fully resolved tree and suggest that plastid DNA is a useful tool for resolving red algal relationships. Lastly, we estimate the evolutionary rates among more than 200 plastid genes, and assess their usefulness for species and subspecies taxonomy by comparison to well-established barcoding markers such as cox1 and rbcL. Overall, these data demonstrates that red algal plastid genomes are easily obtainable using high-throughput sequencing of total genomic DNA, interesting from evolutionary perspectives, and promising in resolving red algal relationships at evolutionarily-deep and species/subspecies levels.

This record has no associated files available for download.

More information

Accepted/In Press date: 8 February 2013
Published date: 25 March 2013
Additional Information: Copyright 2013 Janouskovec et al

Identifiers

Local EPrints ID: 467294
URI: http://eprints.soton.ac.uk/id/eprint/467294
ISSN: 1932-6203
PURE UUID: a5366945-b421-4a7a-952b-ee31741db935
ORCID for Jan Janouskovec: ORCID iD orcid.org/0000-0001-6547-749X

Catalogue record

Date deposited: 05 Jul 2022 16:49
Last modified: 24 Nov 2022 03:04

Export record

Altmetrics

Contributors

Author: Jan Janouskovec ORCID iD
Author: Shao-Lun Liu
Author: Patrick T. Martone
Author: Wilfrid Carre
Author: Catherine Leblanc
Author: Jonas Collen
Author: Patrick J. Keeling

Download statistics

Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.

View more statistics

Atom RSS 1.0 RSS 2.0

Contact ePrints Soton: eprints@soton.ac.uk

ePrints Soton supports OAI 2.0 with a base URL of http://eprints.soton.ac.uk/cgi/oai2

This repository has been built using EPrints software, developed at the University of Southampton, but available to everyone to use.

We use cookies to ensure that we give you the best experience on our website. If you continue without changing your settings, we will assume that you are happy to receive cookies on the University of Southampton website.

×