Amborella trichopoda Assembly and Gene Annotation

About Amborella trichopoda

Amborella trichopoda is a small, tropical shrub endemic to New Caledonia. It is the only species in the genus Amborella, which is the only member of the family Amborellaceae. As the only living species on the sister lineage to all other flowering plants, it is an important reference for studying plant evolution. Individual Amborella trichopoda are usually sprawling understory shrubs, although occasionally they grow up to eight meters high. They have evergreen leaves and small, white to yellow flowers. The species is dioecious; female plants producing carpals and males producing stamens, and individual plants can change sex between flowerings. Unlike nearly all other flowering plants, they do not posses vessel elements for water conduction. Amborella's genome is a relatively compact 870Mb, arranged into 13 chromosome pairs.

Assembly

Amborella's draft genome sequence was published in December, 2013, by the Amborella Genome Project [1,2]. Initial sequencing and contig assembly was performed using a whole-genome shotgun (WGS) strategy. Contigs and scaffold assignments were refined, and superscaffolds constructed from them using evidence from end-sequenced BACs, single-molecule restriction digest (OpGen) experiments, and fluorescent in-situ hybridization (FISH) experiments.

Annotation

Ab initio annotation of genes and repetitive elements was performed using the DAWGPAWS [3] and EVidenceModeler [4] software packages. These annotations were refined through manual comparison with assembled Amborella cDNA transcripts, gene family analyses, and homology studies.

References

  1. Assembly and validation of the genome of the nonmodel basal angiosperm Amborella.
    Chamala S, Chanderbali AS, Der JP, Lan T, Walts B, Albert VA, dePamphilis CW, Leebens-Mack J, Rounsley S, Schuster SC et al. 2013. Science. 342:1516-1517.
  2. The Amborella genome and the evolution of flowering plants.
    2013. Science. 342:1241089.
  3. The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes.
    Estill JC, Bennetzen JL. 2009. Plant Methods. 5:8.
  4. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments.
    Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, Buell CR, Wortman JR. 2008. Genome Biol.. 9:R7.

Picture credit: Scott Zona via Wikimedia Commons: http://commons.wikimedia.org/wiki/File:Amborella_trichopoda_%283173820625%29.jpg

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyAMTR1.0, INSDC Assembly GCA_000471905.1, Jan 2014
Database version90.1
Base Pairs668,218,890
Golden Path Length706,332,640
Genebuild byAGD
Genebuild methodGenerated from ENA annotation
Data sourceAmborella Genome Database

Gene counts

Coding genes27,313
Non coding genes1,071
Small non coding genes1,010
Long non coding genes61
Gene transcripts28,384

About this species