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Current Genetics

, Volume 63, Issue 3, pp 499–507 | Cite as

Hoarding and horizontal transfer led to an expanded gene and intron repertoire in the plastid genome of the diatom, Toxarium undulatum (Bacillariophyta)

  • Elizabeth C. Ruck
  • Samantha R. Linard
  • Teofil Nakov
  • Edward C. Theriot
  • Andrew J. Alverson
Original Article

Abstract

Although the plastid genomes of diatoms maintain a conserved architecture and core gene set, considerable variation about this core theme exists and can be traced to several different processes. Gene duplication, pseudogenization, and loss, as well as intracellular transfer of genes to the nuclear genome, have all contributed to variation in gene content among diatom species. In addition, some noncoding sequences have highly restricted phylogenetic distributions that suggest a recent foreign origin. We sequenced the plastid genome of the marine diatom, Toxarium undulatum, and found that the genome contains three genes (chlB, chlL, and chlN) involved in light-independent chlorophyll a biosynthesis that were not previously known from diatoms. Phylogenetic and syntenic data suggest that these genes were differentially retained in this one lineage as they were repeatedly lost from most other diatoms. Unique among diatoms and other heterokont algae sequenced so far, the genome also contains a large group II intron within an otherwise intact psaA gene. Although the intron is most similar to one in the plastid-encoded psaA gene of some green algae, high sequence divergence between the diatom and green algal introns rules out recent shared ancestry. We conclude that the psaA intron was likely introduced into the plastid genome of T. undulatum, or some earlier ancestor, by horizontal transfer from an unknown donor. This genome further highlights the myriad processes driving variation in gene and intron content in the plastid genomes of diatoms, one of the world’s foremost primary producers.

Keywords

Chlorophyll a Diatoms Intron Plastid psaA Toxarium 

Notes

Acknowledgments

We thank Colton Kessenich for help with the genome assembly; David Chafin, Jeff Pummill, and Pawel Wolinski for providing computational support through the Arkansas High Performance Computing Center (AHPCC); and Suresh Kumar and Jeffrey Lewis for critical comments on an earlier version of the manuscript. This material is based upon work supported by the National Science Foundation (NSF) under Grant No. DEB-1353131 and an award from the Arkansas Biosciences Institute. This research used computational resources available through the AHPCC, which is funded through multiple NSF grants and the Arkansas Economic Development Commission.

Supplementary material

294_2016_652_MOESM1_ESM.pdf (23 kb)
Figure S1. Individual gene phylogenies based on amino acid alignments for the chlB, chlL, and chlN genes. Numbers at nodes are standard bootstrap proportions from 500 pseudoreplicates (PDF 22 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.Department of Biological SciencesUniversity of ArkansasFayettevilleUSA
  2. 2.Section of Integrative BiologyUniversity of Texas at AustinAustinUSA

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