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Metal-Devouring Plant Genomes Get SMRT Treatment with Sequel System: 2016 SMRT Grant Program Winner Results

Thursday, March 23, 2017

SedumAlfrediiBlog readers may recall that last year’s SMRT Grant winner was Renying Zhuo from the Chinese Academy of Forestry. We’re pleased to report that the project is now complete!

Zhuo proposed sequencing the genomes of two strains of the Sedum alfredii plant from the same ecosystem — one that accumulates cadmium ions from polluted soil and one that doesn’t. The goal was to use high-quality assemblies for comparative genomic analysis to determine the genetic mechanisms responsible for this remediation effect.

Plant DNA was sequenced on the Sequel System by RTL Genomics, and genome assembly was performed by Computomics. (We’re also grateful to Sage Science and Experiment, the other co-sponsors of the SMRT Grant program in making this a worldwide democratic event.) Both plant genomes made it into the “1 Mb contig N50 club” (#1MbCtgClub on Twitter), with contig N50s of 1.08 Mb for Sedum alfredii HE and 1.26 Mb for Sedum alfredii NHZ.

Zhuo and his team will now dive into a deep, detailed comparative analysis between the two genomes to identify genes associated with metal accumulation. Ultimately, they hope the results can be used to improve bioremediation efforts for soils contaminated with heavy metals.

Detailed stats for the two plant assemblies from Computomics:

Sedum alfredii HE Sedum alfredii NHZ
Contigs [#] 1042 2486
Contig size [bp] 235739357 397076979
Longest Contigs [bp] 3521758 5719050
Contigs > 1 M [#] 74 117
N50 contig length [bp] 1087129 1256010
L50 contig count [#] 65 91
BUSCO complete [%] 88.5 90.1
BUSCO complete single copy [%] 60.9 21.8
BUSCO complete duplicated [%] 27.6 68.4
BUSCO fragmented [%] 2.4 1.7
BUSCO missing [%] 9.1 8.1

 

Voting is now open for this year’s Plant and Animal SMRT Grant program. Check out the five finalists and cast your vote by April 5!

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