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Genes (Basel). 2018 Mar 28;9(4). pii: E185. doi: 10.3390/genes9040185.

Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes.

Author information

1
Dobzhansky Center for Genome Bioinformatics, St. Petersburg State Universit, Sredniy Prospekt, 41, Vasilievsky Island, 199004 St. Petersburg, Russia. mahajrod@gmail.com.
2
All-Russia Research Institute for Agricultural Microbiology, Podbelskogo sh. 3, Pushkin, 196608 St. Petersburg, Russia. mahajrod@gmail.com.
3
Dobzhansky Center for Genome Bioinformatics, St. Petersburg State Universit, Sredniy Prospekt, 41, Vasilievsky Island, 199004 St. Petersburg, Russia. mikerayko@gmail.com.
4
Dobzhansky Center for Genome Bioinformatics, St. Petersburg State Universit, Sredniy Prospekt, 41, Vasilievsky Island, 199004 St. Petersburg, Russia. ad3002@gmail.com.
5
Dobzhansky Center for Genome Bioinformatics, St. Petersburg State Universit, Sredniy Prospekt, 41, Vasilievsky Island, 199004 St. Petersburg, Russia. eugene.bakin@gmail.com.
6
Dobzhansky Center for Genome Bioinformatics, St. Petersburg State Universit, Sredniy Prospekt, 41, Vasilievsky Island, 199004 St. Petersburg, Russia. dashzhernakova@gmail.com.
7
Department of Biology, Colorado State University, Fort Collins, CO 80523; USA. kasavajhalaprasad@gmail.com.
8
University and Jepson Herbaria, University of California, Berkeley, NC 94720; USA. crushworth@berkeley.edu.
9
Department of Biotechnology, Indian Institute of Technology. Sardar Patel road, 600036 Chennai, India. rbaskar@iitm.ac.in.
10
Department of Plant and Microbial Biology Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008 Zurich; Switzerland. dmitry.smetanin@botinst.uzh.ch.
11
Department of Energy Joint Genome Institute, Walnut Creek, CA 94598; USA. jschmutz@hudsonalpha.org.
12
HudsonAlpha Institute of Biotechnology, Huntsville, AL 35806; USA. jschmutz@hudsonalpha.org.
13
Department of Energy Joint Genome Institute, Walnut Creek, CA 94598; USA. dsrokhsar@gmail.com.
14
Department of Biology, Duke University, Durham, NC 27708-0338; USA. tmo1@duke.edu.
15
Department of Plant and Microbial Biology Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008 Zurich; Switzerland. grossnik@botinst.uzh.ch.
16
Dobzhansky Center for Genome Bioinformatics, St. Petersburg State Universit, Sredniy Prospekt, 41, Vasilievsky Island, 199004 St. Petersburg, Russia. vbrukhin@gmail.com.
17
Department of Plant Embryology and Reproductive Biology, Komarov Botanical Institute RAS, 197376 St. Petersburg, Russia. vbrukhin@gmail.com.

Abstract

Closely related to the model plant Arabidopsis thaliana, the genus Boechera is known to contain both sexual and apomictic species or accessions. Boechera retrofracta is a diploid sexually reproducing species and is thought to be an ancestral parent species of apomictic species. Here we report the de novo assembly of the B. retrofracta genome using short Illumina and Roche reads from 1 paired-end and 3 mate pair libraries. The distribution of 23-mers from the paired end library has indicated a low level of heterozygosity and the presence of detectable duplications and triplications. The genome size was estimated to be equal 227 Mb. N50 of the assembled scaffolds was 2.3 Mb. Using a hybrid approach that combines homology-based and de novo methods 27,048 protein-coding genes were predicted. Also repeats, transfer RNA (tRNA) and ribosomal RNA (rRNA) genes were annotated. Finally, genes of B. retrofracta and 6 other Brassicaceae species were used for phylogenetic tree reconstruction. In addition, we explored the histidine exonuclease APOLLO locus, related to apomixis in Boechera, and proposed model of its evolution through the series of duplications. An assembled genome of B. retrofracta will help in the challenging assembly of the highly heterozygous genomes of hybrid apomictic species.

KEYWORDS:

Boechera; Brassicaceae; annotation; apomixis; assembly; genome

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