Careers in the Plant Sciences

PostDoc Position

Saint Petersburg State University - St. Petersburg, St. Petersburg, Russia

Position Title: PostDoc Position
Position Type: Research Fellow
Application Review Begins: Monday, July 17, 2017
Application Deadline: Sunday, October 15, 2017
Institution: Saint Petersburg State University
Department/Division: Dobzhansky Center for Genome Bioinformatics
Field (e.g., systematics): Boechera genomics and bioinformatics
City: St. Petersburg, St. Petersburg, Russia
General Information: The Dobzhansky Center for Genomic Bioinformatics at the St. Petersburg State University headed by Prof. Stephen O'Brien is advertising a postdoc position in the group of Vladimir Brukhin (http://dobzhanskycenter.spbu.ru/en/archives/staff/vladimir-brukhin).

The research topic: "Sequencing, assembly and annotation of the highly heterozygous genome of the apomictic plant Boechera divaricarpa". Classifiers: Bioinformatics; Molecular and Cellular Biology; Plant Genomics; Plant Developmental Biology.
The project is carried out in cooperation with the Prof. Ueli Grossniklaus (University of Zurich in Switzerland) and Prof. Thomas Mitchell-Olds (Duke University in North Carolina).

Apomixis, defined as the asexual reproduction of plants through seed, could become a key ‘enabling technology’ of immense benefit to agriculture, because it would enable the permanent fixation of heterosis in crop plants.
A better understanding of the molecular basis of apomixis is crucial for yield increases that are required for the sustainable production of biofuels, biomaterials, fibers, food, and feed. Despite the fact that apomixis is considered as one of the key technologies for the improvement of agriculture, it is currently not known what genes control this important trait, nor has the genome of any apomictic species been sequenced (Grossniklaus et al., 2001; Bicknell & Koltunow, 2004; Koltunow & Grossniklaus, 2003, Rodriguez-Leal and Vielle-Calzada, 2012).
We propose sequencing of the genome of Boechera stricta x stricta (divaricarpa), a member of the Brassicaceae (mustard family). The species Boechera divaricarpa includes both apomictic and sexual accessions. We will use the well characterized accession M4B, because it is a diploid apomict (Schranz et al., 2005), characterized by 98-100% formation of seeds with a 2:6 embryo:endosperm ratio (Aliyu, 2010), indicating apomeiosis (absence or omission of meiosis), parthenogenetic development of the unreduced (2n) egg cell, and pseudogamous fertilization of the central cell with unreduced (2n) pollen (self-fertilization).
The genome size of Boechera is relatively small, estimated to be around 230 Mb (Oyama et al., 2008; Sharbel & Mitchell-Olds, 2001). However, due to the highly heterozygous nature of apomictic genomes, the production of a high quality draft genome is not a trivial task. Thus, in this project we will develop novel approaches and bioinformatics tools that will be generally applicable to highly heterozygous genomes as they are often found in genetically diverse outcrossing species or in asexual lineages. We will use a combination of sequencing technologies (Illumina, Pacific Bioscience) and a novel approach for genome assembly based on topological chromatin interaction (Hi-C) data (Grob et al., 2014) that permits assembling a genome up to chromosomal level without need of a detailed genetic map or the sequencing of BAC clones.
B. divaricarpa is hypothesized to have arisen through hybridization between sexual B. stricta and B. retrofracta. Genomic resources for both parental species are available. We will apply comparative approaches to identify apomixis-related genomic regions through a genomic comparison with the ancestral species.
Apomictic B. divaricarpa likely represents a group of lines arisen through independent hybridisation events (Katama et al., 2007) and we plan to re-sequence another apomictic diploid line of B. stricta x stricta in addition to our reference accession ES517. This will allow us to look into peculiarities of hybridisation events, the chromosomal organisation, and the stability of apomictic genomes.
Qualifications/Requirements: PhD in the field of bioinformatics, computer science, molecular genetics, molecular biology or similar fields. The candidate should be familiar with the basic bioinformatic tools, as well as has the ability to quickly learn assemblers such as Platanus, Discovar, etc., to understand the algorithms for assembly of highly heterozygous genomes (~230 MB) without reference, and be interested in plant genomes. Knowledge of the basics programming is highly desirable. The candidate has to be able to talk and write in English, to prioritize work stages, meet deadlines, the ability to work in a group and interact constructively with international partners are important. Skills of writing scientific publications for international peer-reviewed journals are necessry.
Responsibilities: To perform research on genome assembly and annotation. Report to the PI. Paper writing.
Application Instructions (submission methods, etc.): A successful candidate will be appointed at the Dobzhansky Center for Genomic Bioinformatics, SPSU for a period of two years with a possible extension for the third year depending on the obtained results and publishing records.

More detailes about the project and conditions can be obtained from the project PI Dr. Vladimir Brukhin, Email: vbrukhin@gmail.com, tel. +7 (812) 363-61-03.

Interested candiates should send CV, a motivation letter with a statement of experience and scientific interests, and 2-3 letters of recommendation to Vladimir Brukhin email: vbrukhin@gmail.com
Web Link: http://
Compensation Range:
Contact Name: Vladimir Brukhin, vbrukhin@gmail.com