DOI: 10.5061/dryad.3j9kd51h9
title: Genomic assembly of Botyrococcus braunii race B (Metzger et al. 1988) Ayame strain

description: This dataset is a genomic assembly (v1.0) of DNA from a culture of
 Botryococcus braunii race B, Ayame strain. The strain was isolated in 1984
 by Metzger et al Phytochemistry (1988), 27, 1383-1388. The site of
 isolation was Cote d'Ivoire, barrier lake of Ayame, 24th Feb 1984,
 pH5.7 water temp 30.8.  The strain was then cultured in a lab for
 25 years until being selected for this genomic denovo assembly
 project. The strain makes biofuels consisting of methylated triterpenoids
 termed "botryococenes." The project objectives and achievements
 were to selectively identify and assemble full length triterpenoid
 synthase genes, annotate them, determine the numer of paralogues
 in this set of genes, and to investigate their evolution,
 via a bioinformatic process. The annotations of the slected genes
 are housed elsewhere on NCBI as genbank accessions KU248134,
 KU248135, KU248136 and KU248137, while the rest of the assembly
 is documented here. Genes in the assembly are from across the
 entire genome, and commensals that were present in the cultutre
 are also deliberately represented in the datset aswell. The lab leading
 the publication (Ball lab) is a bioremediation lab, and the commensals are
 useful remediation organisms. Further, genes upstream in the triterpenoid
 synthesis pathway othere than the terminal genes that were
 targeted, are in the datset and are of interest to the
 wider molecular microbiology community.
description: The sequencing centre was Illumina R&D Hayward CA, USA.
 The software used was SOAPdenovo 1.04. All other details of culturing and
 the annotation are contained in the FIM paper.
 Briefly, detection of KU248134, KU248135, KU248136 and KU248137
 (contained in this v 1.0 dataset along wih many other genomc loci) was via
 tBlastn at Ncbi, then positive hits were tested via Blastx of pdb at Ncbi.
 Mining was iterative, using each hit as a bait to the assembly, thus
 pulling out the entire set of paralogues. Other baits included: green
 algal squalene synthase fromm <em>B. braunii</em>,
 <em>Chlamydomons reinhardtii</em>, and <em>Volvox
 carteri</em>. Annotation was manual, and intron-exon and exon-intron
 boundaries were identified manually as described in the FIM paper. 
 Introns were crossed by means of 2kb and 4kb paired-end libnraries
 seuenced at Illumina. The objective and acheivement was to cross introns
 to link exons, rather than sequencing in full through introns. Rigorous
 assembly by SOAP denovo, with tight constraints confirmed
 that exonic regions had been reliably contigged together. Analysis was via
 phylogentic tree building, using four programs that each gave solid
 bootstrap support for a gene branching order. These phylogentic programs
 were TNT, FastME p-distance, UPGMA Poisson, and ProtPars. An evolutionary
 scenario or model was suggested for the order and drivers of the gene
 duplications involved, beginning from a squalene synthase gene. Processing
 of the genomic dataset as a whole is ongoing. The dataset in assembly v1.0
 is also a suitable comparator dataset to assemblies
 other <em>B.braunii</em> genomes, of which there is at least
 one other to date.
description: The dataset is intended as a repository for supplementary data
 pertaining to a manuscript submitted to Frontiers in Microbiology in Feb
 2021: Robert B Moore, Michael Barnathan, Brian
 Fristensky, Yan Li, Gregory Knowles, Paul Gardner-Stephen, Angelo Bueti,
 Peter Anderson, Jian G Qin, and Andrew S Ball (2021 Submitted). Parsimony
 and distance approaches resolve a triterpenoid synthase gene tree in a
 green algal species tree of squalene sythases. Frontiers In
 Microbiology. The user would optimally want to know
 what reader to view the text in, being that the text is of a total of
 ~500Mb and so too big for most word processors to open.
 We suggest viewing in the free text editor "EditPad Lite
 8" available free from: https://www.editpadlite.com/download.html