ORCID Profile
0000-0002-6659-1363
Current Organisation
University of Queensland
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Publisher: Cold Spring Harbor Laboratory
Date: 11-09-2021
DOI: 10.1101/2021.09.09.459704
Abstract: Recent advances in the sequencing and assembly of plant genomes have allowed the generation of genomes with increasing contiguity and sequence accuracy. The chromosome level assembly of the contigs generated from long read sequencing has involved the use of proximity analysis (Hi-C) or traditional genetic maps to guide the placement of sequence contigs within chromosomes. The development of highly accurate long reads by repeated sequencing of circularized DNA (PacBio HiFi) has greatly increased the size of contigs. We now report the use of HiFiasm to assemble the genome of Macadamia jansenii . a genome that has been used as model to test sequencing and assembly. This achieved almost complete chromosome level assembly from the sequence data alone without the need for higher level chromosome map information. Eight of the 14 chromosomes were represented by a single large contig and the other 6 assembled into 2-4 main contigs. The small number of chromosome breaks appear to be due to highly repetitive regions of ribosomal genes that cannot be assembled by these approaches. De novo assembly of near complete chromosome level plant genomes now seems possible using these sequencing and assembly tools. Further targeted strategies might allow these remaining gaps to be closed. De novo assembly of near complete chromosome level plant genomes is now possible using current long read sequencing and assembly tools.
Publisher: Springer Science and Business Media LLC
Date: 06-08-2012
DOI: 10.1038/SREP00557
Publisher: Wiley
Date: 08-10-2021
DOI: 10.1111/TPJ.15509
Abstract: Most flowering plants are hermaphrodites, but around 6% of species are dioecious, having separate male and female plants. Sex chromosomes and some sex‐specific genes have been reported in plants, but the genome sequences have not been compared. We now report the genome sequence of male and female jojoba ( Simmondsia chinensis ) plants, revealing a very large difference in the sex chromosomes. The male genome assembly was 832 Mb and the female 822 Mb. This was explained by the large size differences in the Y chromosome (37.6 Mb) compared with the X chromosome (26.9 Mb). Relative to the X chromosome, the Y chromosome had two large insertions each of more than 5 Mb containing more than 400 genes. Many of the genes in the chromosome‐specific regions were novel. These male‐specific regions included many flowering‐related and stress response genes. Smaller insertions found only in the X chromosome totalled 877 kb. The wide ergence of the sex chromosomes suggests a long period of adaptation to erging sex‐specific roles. Male and female plants may have evolved to accommodate factors such as differing reproductive resource allocation requirements under the stress of the desert environment in which the plants are found. The sex‐determining regions accumulate genes beneficial to each sex. This has required the evolution of many more novel sex‐specific genes than has been reported for other organisms. This suggest that dioecious plants provide a novel source of genes for manipulation of reproductive performance and environmental adaptation in crops.
Publisher: Cold Spring Harbor Laboratory
Date: 09-09-2021
DOI: 10.1101/2021.09.08.459545
Abstract: Macadamia, a recently domesticated expanding nut crop in the tropical and subtropical regions of the world, is one of the most economically important genera in the erse and widely adapted Proteaceae family. All four species of Macadamia are rare in the wild with the most recently discovered, M. jansenii , being endangered. The M. jansenii genome has been used as a model for testing sequencing methods using a wide range of long read sequencing techniques. Here we report a chromosome level genome assembly, generated using a combination of Pacific Biosciences sequencing and Hi-C, comprising 14 pseudo-molecules, with a N50 of 58 Mb and a total 758 Mb genome assembly size of which 56% is repetitive. Completeness assessment revealed that the assembly covered 96.9% of the conserved single copy genes. Annotation predicted 31,591 protein coding genes and allowed the characterization of genes encoding biosynthesis of cyanogenic glycosides, fatty acid metabolism and anti-microbial proteins. Re-sequencing of seven other genotypes confirmed low ersity and low heterozygosity within this endangered species. Important morphological characteristics of this species such as small tree size and high kernel recovery suggest that M. jansenii is an important source of these commercial traits for breeding. As a member of a small group of families that are sister to the core eudicots, this high-quality genome also provides a key resource for evolutionary and comparative genomics studies.
Publisher: GigaScience Press
Date: 10-06-2021
DOI: 10.46471/GIGABYTE.24
Abstract: Advances in DNA sequencing have made it easier to sequence and assemble plant genomes. Here, we extend an earlier study, and compare recent methods for long read sequencing and assembly. Updated Oxford Nanopore Technology software improved assemblies. Using more accurate sequences produced by repeated sequencing of the same molecule (Pacific Biosciences HiFi) resulted in less fragmented assembly of sequencing reads. Using data for increased genome coverage resulted in longer contigs, but reduced total assembly length and improved genome completeness. The original model species, Macadamia jansenii, was also compared with three other Macadamia species, as well as avocado (Persea americana) and jojoba (Simmondsia chinensis). In these angiosperms, increasing sequence data volumes caused a linear increase in contig size, decreased assembly length and further improved already high completeness. Differences in genome size and sequence complexity influenced the success of assembly. Advances in long read sequencing technology continue to improve plant genome sequencing and assembly. However, results were improved by greater genome coverage, with the amount needed to achieve a particular level of assembly being species dependent.
Publisher: Springer Science and Business Media LLC
Date: 21-10-2012
DOI: 10.1007/S12038-012-9253-Z
Abstract: Advances in DNA sequencing provide tools for efficient large-scale discovery of markers for use in plants. Discovery options include large-scale licon sequencing, transcriptome sequencing, gene-enriched genome sequencing and whole genome sequencing. Ex les of each of these approaches and their potential to generate molecular markers for specific applications have been described. Sequencing the whole genome of parents identifies all the polymorphisms available for analysis in their progeny. Sequencing PCR licons of sets of candidate genes from DNA bulks can be used to define the available variation in these genes that might be exploited in a population or germplasm collection. Sequencing of the transcriptomes of genotypes varying for the trait of interest may identify genes with patterns of expression that could explain the phenotypic variation. Sequencing genomic DNA enriched for genes by hybridization with probes for all or some of the known genes simplifies sequencing and analysis of differences in gene sequences between large numbers of genotypes and genes especially when working with complex genomes. Ex les of application of the above-mentioned techniques have been described.
Publisher: Wiley
Date: 12-2021
DOI: 10.1002/PLD3.364
Abstract: Macadamia, a recently domesticated expanding nut crop in the tropical and subtropical regions of the world, is one of the most economically important genera in the erse and widely adapted Proteaceae family. All four species of Macadamia are rare in the wild with the most recently discovered, M. jansenii , being endangered. The M. jansenii genome has been used as a model for testing sequencing methods using a wide range of long read sequencing techniques. Here, we report a chromosome level genome assembly, generated using a combination of Pacific Biosciences sequencing and Hi‐C, comprising 14 pseudo‐molecules, with a N50 of 52 Mb and a total genome assembly size of 758 Mb of which 56% is repetitive. Completeness assessment revealed that the assembly covered −97.1% of the conserved single copy genes. Annotation predicted 31,591 protein coding genes and allowed the characterization of genes encoding biosynthesis of cyanogenic glycosides, fatty acid metabolism, and anti‐microbial proteins. Re‐sequencing of seven other genotypes confirmed low ersity and low heterozygosity within this endangered species. Important morphological characteristics of this species such as small tree size and high kernel recovery suggest that M. jansenii is an important source of these commercial traits for breeding. As a member of a small group of families that are sister to the core eudicots, this high‐quality genome also provides a key resource for evolutionary and comparative genomics studies.
Publisher: Wiley
Date: 02-12-2021
DOI: 10.1111/TPJ.15583
Abstract: Recent advances in the sequencing and assembly of plant genomes have allowed the generation of genomes with increasing contiguity and sequence accuracy. Chromosome level genome assemblies using sequence contigs generated from long read sequencing have involved the use of proximity analysis (Hi‐C) or traditional genetic maps to guide the placement of sequence contigs within chromosomes. The development of highly accurate long reads by repeated sequencing of circularized DNA (HiFi PacBio) has greatly increased the size of contigs. We now report the use of HiFiasm to assemble the genome of Macadamia jansenii , a genome that has been used as a model to test sequencing and assembly. This achieved almost complete chromosome level assembly from the sequence data alone without the need for higher level chromosome map information. Eight of the 14 chromosomes were represented by a single large contig (six with telomere repeats at both ends) and the other six assembled from two to four main contigs. The small number of chromosome breaks appears to be the result of highly repetitive regions including ribosomal genes that cannot be assembled by these approaches. De novo assembly of near complete chromosome level plant genomes now appears possible using these sequencing and assembly tools. Further targeted strategies might allow these remaining gaps to be closed.
Publisher: Southern Cross Publishing
Date: 20-05-2017
Publisher: Springer Science and Business Media LLC
Date: 11-2005
Publisher: Cold Spring Harbor Laboratory
Date: 25-09-2023
Publisher: Wiley
Date: 07-06-2011
DOI: 10.1111/J.1467-7652.2011.00629.X
Abstract: High-throughput sequencing of pooled DNA was applied to polymorphism discovery in candidate genes involved in starch synthesis. This approach employed semi- to long-range PCR (LR-PCR) followed by next-generation sequencing technology. A total of 17 rice starch synthesis genes encoding seven classes of enzymes, including ADP-glucose pyrophosphorylase (AGPase), granule starch synthase (GBSS), soluble starch synthase (SS), starch branching enzyme (BE), starch debranching enzyme (DBE) and starch phosphorylase (SPHOL) and phosphate translocator (GPT1) from 233 genotypes were PCR lified using semi- to long-range PCR. The lification products were equimolarly pooled and sequenced using massively parallel sequencing technology (MPS). By detecting single nucleotide polymorphism (SNP)/Indels in both coding and noncoding areas of the genes, we identified genetic differences and characterized the SNP/Indel variation and distribution patterns among in idual starch candidate genes. Approximately, 60.9 million reads were generated, of which 54.8 million (90%) mapped to the reference sequences. The average coverage rate ranged from 12,708 to 38,300 times for SSIIa and SSIIIb, respectively. SNPs and single/multiple-base Indels were analysed in a total assembled length of 116,403 bp. In total, 501 SNPs and 113 Indels were detected across the 17 starch-related loci. The ratio of synonymous to nonsynonymous SNPs (Ka/Ks) test indicated GBSSI and isoamylase 1 (ISA1) as the least ersified (most purified) and conservative genes as the studied populations have been through cycles of selection. This report demonstrates a useful strategy for screening germplasm by MPS to discover variants in a specific target group of genes.
Publisher: Elsevier BV
Date: 07-2010
DOI: 10.1016/J.JTBI.2010.04.017
Abstract: Granule Bound Starch Synthase I (GBSSI), which influences the grain quality of cereals and, particularly, rice, is one of the most important plant genes. Using GBSSI as a model plant gene in this study, we examined a number of different computational algorithm tools and programs to explore the functional SNPs of this important rice gene and the possible relationships between genetic mutation and phenotypic variation. A total of 51 SNPs/indels were retrieved from databases, including three important coding non-synonymous SNPs, namely those in exons 6, 9 and 10. Sorting Intolerant from Tolerant (SIFT) results showed that a candidate [C/A] SNP (ID: OryzaSNP2) in exon 6 (coordinate 2494) is the most important non-synonymous SNP with the highest phenotypic impact on waxy protein. This SNP can alter a tyrosine to serine residue at position 224 of waxy protein. Computational simulation of GBSSI protein with the Geno3D suggested that this mutant SNP creates a bigger loop on the surface of waxy protein and results in a shape different from that of native GBSSI. Here, we suggest a potential transcriptional binding factor site (TBF8) which has one [C/T] SNP [rs53176842] at coordinate 2777 in boundary site of intron 7/exon 8, according to Transcriptional Factor (TF) search analysis. This SNP might potentially have a major effect on regulation and function of GBSSI. Combining SNP mining data and in silico structural analysis of waxy protein led us to prepare an efficient computational pathway which can be applied for other plant genes.
Publisher: Wiley
Date: 13-04-2009
DOI: 10.1111/J.1467-7652.2009.00411.X
Abstract: The application of single nucleotide polymorphisms (SNPs) in plant breeding involves the analysis of a large number of s les, and therefore requires rapid, inexpensive and highly automated multiplex methods to genotype the sequence variants. We have optimized a high-throughput multiplexed SNP assay for eight polymorphisms which explain two agronomic and three grain quality traits in rice. Gene fragments coding for the agronomic traits plant height (semi-dwarf, sd-1) and blast disease resistance (Pi-ta) and the quality traits amylose content (waxy), gelatinization temperature (alk) and fragrance (fgr) were lified in a multiplex polymerase chain reaction. A single base extension reaction carried out at the polymorphism responsible for each of these phenotypes within these genes generated extension products which were quantified by a matrix-assisted laser desorption ionization-time of flight system. The assay detects both SNPs and indels and is co-dominant, simultaneously detecting both homozygous and heterozygous s les in a multiplex system. This assay analyses eight functional polymorphisms in one 5 microL reaction, demonstrating the high-throughput and cost-effective capability of this system. At this conservative level of multiplexing, 3072 assays can be performed in a single 384-well microtitre plate, allowing the rapid production of valuable information for selection in rice breeding.
Location: Iran (Islamic Republic of)
Location: Iran (Islamic Republic of)
Location: Iran (Islamic Republic of)
No related grants have been discovered for Ardashir Kharabian-Masouleh.