The complete chloroplast genome of banana (Musa acuminata, Zingiberales): insight into plastid monocotyledon evolution

PLoS One. 2013 Jun 28;8(6):e67350. doi: 10.1371/journal.pone.0067350. Print 2013.

Abstract

Background: Banana (genus Musa) is a crop of major economic importance worldwide. It is a monocotyledonous member of the Zingiberales, a sister group of the widely studied Poales. Most cultivated bananas are natural Musa inter-(sub-)specific triploid hybrids. A Musa acuminata reference nuclear genome sequence was recently produced based on sequencing of genomic DNA enriched in nucleus.

Methodology/principal findings: The Musa acuminata chloroplast genome was assembled with chloroplast reads extracted from whole-genome-shotgun sequence data. The Musa chloroplast genome is a circular molecule of 169,972 bp with a quadripartite structure containing two single copy regions, a Large Single Copy region (LSC, 88,338 bp) and a Small Single Copy region (SSC, 10,768 bp) separated by Inverted Repeat regions (IRs, 35,433 bp). Two forms of the chloroplast genome relative to the orientation of SSC versus LSC were found. The Musa chloroplast genome shows an extreme IR expansion at the IR/SSC boundary relative to the most common structures found in angiosperms. This expansion consists of the integration of three additional complete genes (rps15, ndhH and ycf1) and part of the ndhA gene. No such expansion has been observed in monocots so far. Simple Sequence Repeats were identified in the Musa chloroplast genome and a new set of Musa chloroplastic markers was designed.

Conclusion: The complete sequence of M. acuminata ssp malaccensis chloroplast we reported here is the first one for the Zingiberales order. As such it provides new insight in the evolution of the chloroplast of monocotyledons. In particular, it reinforces that IR/SSC expansion has occurred independently several times within monocotyledons. The discovery of new polymorphic markers within Musa chloroplast opens new perspectives to better understand the origin of cultivated triploid bananas.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Codon
  • Evolution, Molecular
  • Genes, Plant
  • Genetic Markers
  • Genome, Chloroplast*
  • Likelihood Functions
  • Microsatellite Repeats
  • Molecular Sequence Annotation
  • Musa / genetics*
  • Phylogeny
  • Plastids / genetics*
  • Polymorphism, Genetic
  • Sequence Analysis, DNA
  • Triploidy

Substances

  • Codon
  • Genetic Markers

Grant support

Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), French National Research Agency (ANR) and Commissariat à l'Energie Atomique (CEA). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.