De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq

<p>Abstract</p> <p>Background</p> <p><it>De novo </it>assembly of transcript sequences produced by short-read DNA sequencing technologies offers a rapid approach to obtain expressed gene catalogs for non-model organisms. A draft genome sequence will be produced in 2010 for a <it>Eucalyptus </it>tree species (<it>E. grandis</it>) representing the most important hardwood fibre crop in the world. Genome annotation of this valuable woody plant and genetic dissection of its superior growth and productivity will be greatly facilitated by the availability of a comprehensive collection of expressed gene sequences from multiple tissues and organs.</p> <p>Results</p> <p>We present an extensive expressed gene catalog for a commercially grown <it>E. grandis </it>× <it>E. urophylla </it>hybrid clone constructed using only Illumina mRNA-Seq technology and <it>de novo </it>assembly. A total of 18,894 transcript-derived contigs, a large proportion of which represent full-length protein coding genes were assembled and annotated. Analysis of assembly quality, length and diversity show that this dataset represent the most comprehensive expressed gene catalog for any <it>Eucalyptus </it>tree. mRNA-Seq analysis furthermore allowed digital expression profiling of all of the assembled transcripts across diverse xylogenic and non-xylogenic tissues, which is invaluable for ascribing putative gene functions.</p> <p>Conclusions</p> <p><it>De novo </it>assembly of Illumina mRNA-Seq reads is an efficient approach for transcriptome sequencing and profiling in <it>Eucalyptus </it>and other non-model organisms. The transcriptome resource (Eucspresso, <url>http://eucspresso.bi.up.ac.za/</url>) generated by this study will be of value for genomic analysis of woody biomass production in <it>Eucalyptus </it>and for comparative genomic analysis of growth and development in woody and herbaceous plants.</p

Genetic diversity and population structure analysis reveals the unique genetic composition of South African selected macadamia accessions

Macadamia nuts are known globally for their high quality and economic value. Global macadamia commercial nut production amounts to 60,000 metric tonnes and is increasing steadily. South Africa is the leading producer with 29% of worldwide kernel production. Commercial macadamia germplasm was originally selected from a small genepool (mainly Macadamia integrifolia species) from a limited geographic distribution in Australia. These accessions were subsequently bred, cloned and exported across the world to start local macadamia industries. The South African macadamia industry was established with pre-commercial and commercial macadamia from different parts of the world, and local selections were also performed. Many of these accessions have unique genetic compositions that have not been characterized yet. We used 13 nuclear microsatellite markers to study the genetic diversity and structure of macadamia germplasm cultivated in South Africa. We compared four groups of accessions including 31 originating from the Hawaiian Agricultural Experimental Station (HAES), 19 from Australia (AUS), two from California and one from Israel (OTH), 31 from South Africa’s locally selected accessions (SA) and 26 from two local Farmers (FARM). We used STRUCTURE, PCoA and neighbour-joining phylogenetic analyses to show that the South African selected accessions include diverse hybrid genotypes with strong Macadamia tetraphylla composition, unlike the Hawaiian commercially released and Australian representative collections that mostly have M. integrifolia or hybrid composition. Our results suggest that the South African selections represent a unique and diverse set of germplasm for future macadamia improvement efforts that will benefit from genomic breeding technologies.The National Research Foundation (NRF) of South Africa and Macadamias South Africa.https://link.springer.com/journal/11295hj2023BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Functional network analysis of genes differentially expressed during xylogenesis in soc1ful woody Arabidopsis plants

Many plant genes are known to be involved in the development of cambium and wood, but how the expression and functional interaction of these genes determine the unique biology of wood remains largely unknown. We used the soc1ful loss of function mutant – the woodiest genotype known in the otherwise herbaceous model plant Arabidopsis – to investigate the expression and interactions of genes involved in secondary growth (wood formation). Detailed anatomical observations of the stem in combination with mRNA sequencing were used to assess transcriptome remodeling during xylogenesis in wild-type and woody soc1ful plants. To interpret the transcriptome changes, we constructed functional gene association networks of differentially expressed genes using the STRING database. This analysis revealed functionally enriched gene association hubs that are differentially expressed in herbaceous and woody tissues. In particular, we observed the differential expression of genes related to mechanical stress and jasmonate biosynthesis/ signaling during wood formation in soc1ful plants that may be an effect of greater tension within woody tissues. Our results suggest that habit shifts from herbaceous to woody life forms observed in many angiosperm lineages could have evolved convergently by genetic changes that modulate the gene expression and interaction network, and thereby redeploy the conserved wood developmental program.The Naturalis Biodiversity Center (FES 017/202), the Alberta Mennega Stichting, the Genome Canada Large-Scale Applied Research Program (POPCAN, project 168BIO), USDA National Institute of Food and Agriculture and AgBioResearch to PPE, a NSERC (Canada) Discovery Grant to CJD and NWO (Netherlands Science Foundation) VIDI and Ecogenomics grants to MES.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1365-313Xhb2016Genetic

Guidelines for the vaccination of HIV-infected adolescents and adults in South Africa

No abstract available

Bin mapping of tomato diversity array (DArT) markers to genomic regions of Solanum lycopersicum × Solanum pennellii introgression lines

Marker-trait association studies in tomato have progressed rapidly due to the availability of several populations developed between wild species and domesticated tomato. However, in the absence of whole genome sequences for each wild species, molecular marker methods for whole genome comparisons and fine mapping are required. We describe the development and validation of a diversity arrays technology (DArT) platform for tomato using an introgression line (IL) population consisting of wild Solanumpennellii introgressed into Solanumlycopersicum (cv. M82). A tomato diversity array consisting of 6,912 clones from domesticated tomato and twelve wild tomato/Solanaceous species was constructed. We successfully bin-mapped 990 polymorphic DArT markers together with 108 RFLP markers across the IL population, increasing the number of markers available for each S.pennellii introgression by tenfold on average. A subset of DArT markers from ILs previously associated with increased levels of lycopene and carotene were sequenced, and 44% matched protein coding genes. The bin-map position and order of sequenced DArT markers correlated well with their physical position on scaffolds of the draft tomato genome sequence (SL2.40). The utility of sequenced DArT markers was illustrated by converting several markers in both the S.pennellii and S.lycopersicum phases to cleaved amplified polymorphic sequence (CAPS) markers. Genotype scores from the CAPS markers confirmed the genotype scores from the DArT hybridizations used to construct the bin map. The tomato diversity array provides additional “sequence-characterized” markers for fine mapping of QTLs in S.pennellii ILs and wild tomato species

Genomic population structure and prevalence of copy number variations in South African Nguni cattle

CITATION: Wang, M. D., Dzama, K., Hefer, C. A. & Muchadeyi, F. C. 2015. Genomic population structure and prevalence of copy number variations in South African Nguni cattle. BMC Genomics, 16:894, doi:10.1186/s12864-015-2122-z.The original publication is available at http://bmcgenomics.biomedcentral.comBackground: Copy number variations (CNVs) are modifications in DNA structure comprising of deletions, duplications, insertions and complex multi-site variants. Although CNVs are proven to be involved in a variety of phenotypic discrepancies, the full extent and consequence of CNVs is yet to be understood. To date, no such genomic characterization has been performed in indigenous South African Nguni cattle. Nguni cattle are recognized for their ability to sustain harsh environmental conditions while exhibiting enhanced resistance to disease and parasites and are thought to comprise of up to nine different ecotypes. Methods: Illumina BovineSNP50 Beadchip data was utilized to investigate genomic population structure and the prevalence of CNVs in 492 South African Nguni cattle. PLINK, ADMIXTURE, R, gPLINK and Haploview software was utilized for quality control, population structure and haplotype block determination. PennCNV hidden Markov model identified CNVs and genes contained within and 10 Mb downstream from reported CNVs. PANTHER and Ensembl databases were subsequently utilized for gene annotation analyses. Results: Population structure analyses on Nguni cattle revealed 5 sub-populations with a possible sub-structure evident at K equal to 8. Four hundred and thirty three CNVs that formed 334 CNVRs ranging from 30 kb to 1 Mb in size are reported. Only 231 of the 492 animals demonstrated CNVRs. Two hundred and eighty nine genes were observed within CNVRs identified. Of these 149, 28, 44, 2 and 14 genes were unique to sub-populations A, B, C, D and E respectively. Gene ontology analyses demonstrated a number of pathways to be represented by respective genes, including immune response, response to abiotic stress and biological regulation processess. Conclusions: CNVs may explain part of the phenotypic diversity and the enhanced adaptation evident in Nguni cattle. Genes involved in a number of cellular components, biological processes and molecular functions are reported within CNVRs identified. The significance of such CNVRs and the possible effect thereof needs to be ascertained and may hold interesting insight into the functional and adaptive consequence of CNVs in cattle.http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-2122-zPublisher's versio

Data from: Genomic and functional approaches reveal a case of adaptive introgression from Populus balsamifera (balsam poplar) in P. trichocarpa (black cottonwood)

Natural hybrid zones in forest trees provide systems to study the transfer of adaptive genetic variation by introgression. Previous landscape genomic studies in Populus trichocarpa, a keystone tree species, indicated genomic footprints of admixture with its sister species P. balsamifera and identified candidate genes for local adaptation. Here, we explored patterns of introgression and signals of local adaptation in P. trichocarpa and P. balsamifera, employing genome resequencing data from three chromosomes in pure species and admixed individuals from wild populations. Local ancestry analysis in admixed P. trichocarpa revealed a telomeric region in chromosome 15 with P. balsamifera ancestry, containing several candidate genes for local adaptation. Genomic analyses revealed signals of selection in certain genes in this region (e.g. PRR5, COMT1), and functional analyses based on gene expression variation and correlations with adaptive phenotypes suggest distinct functions of the introgressed alleles. In contrast, a block of genes in chromosome 12 paralogous to the introgressed region showed no signs of introgression or signatures of selection. We hypothesize that the introgressed region in chromosome 15 has introduced modular, or cassette-like variation into P. trichocarpa. These linked adaptive mutations are associated with a block of genes in chromosome 15 that appear to have undergone neo- or sub-functionalization relative to paralogs in a duplicated region on chromosome 12 that show no signatures of adaptive variation. The association between P. balsamifera introgressed alleles with the expression of adaptive traits in P. trichocarpa supports the hypothesis that this is a case of adaptive introgression in an ecologically important foundation species

Populus-aligned plastome sequence alignments

WGS short reads were aligned to the Nisqually-1 chloroplast reference genome (GenBank: EF489041.1) using BWA version 0.6.2. For each position in the reference plastome, bases were called only if the coverage was greater than 1000 reads, as the average read depth for each base pair was 7000 or greater. To improve accuracy, bases were only called if the 1000+ calls agreed for either the reference or alternate base for at least 80% of the reads. Any position not meeting these criteria was called as missing data. Indels were excluded for all analyses