Biology subjects

Topp, B.

Publications and source records attributed to Topp, B..

8 recordsLinked to original sources

bioRxiv2025

Genetic diversity and variation in heterozygosity in Macadamia

BackgroundMacadamia is a diploid (2n =28) rainforest tree of the Proteaceae family, native to Australia. Single-nucleotide polymorphisms (SNPs) have proven to be effective tools for evaluating genetic diversity and heterozygosity. SNPs from the whole genome were used to determine allelic diversity within different species and breeding populations, and to investigate the heterozygosity of genotypes ResultsA total of 349 samples, including wild and domesticated genotypes, were whole genome sequenced, generating 4,180,786 - 7,661,269, 2,446,762 - 7,356,187, 2,829,944 - 4,391,600, 1601519 - 3,182,089 and 3,123,715 to 9,620,640 single nucleotide polymorphism (SNP) positions at the whole genome level for M. integrifolia, M. tetraphylla, M. ternifolia, M. jansenii and the domesticated cultivars and breeding selections respectively. The overall SNP diversity for wild M. integrifolia, M. tetraphylla, M. ternifolia and M. jansenii was 4.43%, 4.33%, 1.80% and 1.1%, respectively. Domesticated M. integrifolia showed an overall SNP diversity of 3.4%, 1.03% lower than wild M. integrifolia, providing evidence of a genetic bottleneck during domestication. Genetic diversity at the individual level for the domesticated gene pool varied from 0.4% to 1.24%, with an overall diversity of 6.10%. Results across different breeding groups revealed that the Australian breeding selections (NMBPA) had the highest diversity, and HAES cultivars had the lowest diversity. Wild M. integrifolia and M. tetraphylla exhibited heterozygosity ranging from 0.36% to 0.71% and 0.30% to 0.71% respectively. The two non-edible species, M. ternifolia and M. jansenii, displayed relatively low heterozygosity (From 0.29% to 0.42% and 0.19% to 0.34% respectively). Domesticated macadamia exhibited a wide range of heterozygosity (0.33% to 1.15%). Additionally, heterozygosity correlated with yield efficiency (kernel yield/tree volume), cumulative kernel yield at age 8 and cumulative nut in shell (NIS) yield at age 8 and showed that performance increased with heterozygosity to an optimal level and declined thereafter. ConclusionThese findings confirmed that there is substantial genetic variation among the different macadamia genotypes. The results also revealed that the greatest diversity is present in wild germplasm. The data will greatly support future genome-wide studies and breeding programs.

plant biology↗

bioRxiv2024

Analysis of genetic variation in Macadamia shows evidence of extensive reticulate evolution

The genus Macadamia in the Proteaceae family includes four species. To explore diversity in macadamia genetic resources, a total of 166 wild genotypes, representing all four species, were sequenced. The four species were clearly distinguished as four separate clades in a phylogenetic analysis of nuclear gene CDS. M. integrifolia and M. tetraphylla formed a clade that had diverged from a clade including M. ternifolia and M. jansenii. The greatest diversity in nuclear and chloroplast genomes was found in the more widely distributed M. integrifolia while the rare M. jansenii showed little diversity. The chloroplast phylogeny revealed a much more complex evolutionary history. Multiple chloroplast capture events have resulted in chloroplast genome clades including genotypes from different species. This suggests extensive reticulate evolution in Macadamia despite the emergence of the four distinct species that are supported by the analysis of their nuclear genomes. The chloroplast genomes showed strong associations with geographical distribution reflecting limited maternal gene movement in these species having large seeds. The nuclear genomes showed lesser geographical differences, probably reflecting longer distance movement of pollen. This improved understanding of the distribution of diversity in Macadamia will aid conservation of these rare species now found in highly fragmented rainforest remnants. HighlightsWhole genome sequencing of population of the four species in the Macadamia genus allowed phylogenetic relationships to be determined and revealed significant reticulate evolution.

evolutionary biology↗

bioRxiv2023

The genomes of the Macadamia genus

Macadamia, a genus native to Eastern Australia, comprises four species, Macadamia integrifolia, M. tetraphylla, M. ternifolia, and M. jansenii. Macadamia was recently domesticated largely from a limited gene pool of Hawaiian germplasm and has become a commercially significant nut crop. Disease susceptibility and climate adaptability challenges, highlight the need for use of a wider range of genetic resources for macadamia production. High quality haploid resolved genome assemblies were generated using HiFiasm to allow comparison of the genomes of the four species. Assembly sizes ranged from 735 Mb to 795 Mb and N50 from 53.7 Mb to 56 Mb, indicating high assembly continuity with most of the chromosomes covered telomere to telomere. Repeat analysis revealed that approximately 61% of the genomes were repetitive sequence. The BUSCO completeness scores ranged from 95.0% to 98.9%, confirming good coverage of the genomes. Gene prediction identified 37198 to 40534 genes. The ks distribution plot of Macadamia and Telopea suggests Macadamia has undergone a whole genome duplication event prior to divergence of the four species and that Telopea genome was duplicated more recently. Synteny analysis revealed a high conservation and similarity of the genome structure in all four species. Differences in the content of genes of fatty acid and cyanogenic glycoside biosynthesis were found between the species. An antimicrobial gene with a conserved cysteine motif was found in all four species. The four genomes provide reference genomes for exploring genetic variation across the genus in wild and domesticated germplasm to support plant breeding.

genomics↗

bioRxiv2021

De-novo chromosome level assembly of plant genomes from long read sequence data

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. Significance statement (of up to two sentences)De novo assembly of near complete chromosome level plant genomes is now possible using current long read sequencing and assembly tools.

genomics↗

bioRxiv2021

The genome of the endangered Macadamia jansenii displays little diversity but represents an 1 important genetic resource for plant breeding

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 diverse 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 diversity 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.

genomics↗

bioRxiv2021

Improvements in the Sequencing and Assembly of Plant Genomes

BackgroundAdvances in DNA sequencing have reduced the difficulty of sequencing and assembling plant genomes. A range of methods for long read sequencing and assembly have been recently compared and we now extend the earlier study and report a comparison with more recent methods. ResultsUpdated Oxford Nanopore Technology software supported improved assemblies. The use of more accurate sequences produced by repeated sequencing of the same molecule (PacBio HiFi) resulted in much less fragmented assembly of sequencing reads. The use of more data to give increased genome coverage resulted in longer contigs (higher N50) but reduced the total length of the assemblies and improved genome completeness (BUSCO). The original model species, Macadamia jansenii, a basal eudicot, was also compared with the 3 other Macadamia species and with avocado (Persea americana), a magnoliid, and jojoba (Simmondsia chinensis) a core eudicot. In these phylogenetically diverse angiosperms, increasing sequence data volumes also caused a highly linear increase in contig size, decreased assembly length and further improved already high completeness. Differences in genome size and sequence complexity apparently influenced the success of assembly from these different species. ConclusionsAdvances in long read sequencing technology have continued to significantly improve the results of sequencing and assembly of plant genomes. However, results were consistently improved by greater genome coverage (using an increased number of reads) with the amount needed to achieve a particular level of assembly being species dependant.

genomics↗

bioRxiv2020

Chromosome-scale assembly and annotation of the macadamia genome(Macadamia integrifolia HAES 741)

Macadamia integrifolia is a representative of the large basal eudicot family Proteaceae and the main progenitor species of the Australian native nut crop macadamia. Since its commercialisation in Hawaii fewer than 100 years ago, global production has expanded rapidly. However, genomic resources are limited in comparison to other horticultural crops. The first draft assembly of M. integrifolia had good coverage of the functional gene space but its high fragmentation has restricted its use in comparative genomics and association studies. Here we have generated an improved assembly of cultivar HAES 741 (4,094 scaffolds, 745 Mb, N50 413 kb) using a combination of Illumina paired and PacBio long read sequences. Scaffolds were anchored to 14 pseudo-chromosomes using seven genetic linkage maps. This assembly has improved contiguity and coverage, with >120 Gb of additional sequence. Following annotation, 34,274 protein-coding genes were predicted, representing 92% of the expected gene content. Our results indicate that the macadamia genome is repetitive and heterozygous. The total repeat content was 55% and genome-wide heterozygosity, estimated by read mapping, was 0.98% or one SNP per 102 bp. This is the first chromosome-scale genome assembly for macadamia and the Proteaceae. It is expected to be a valuable resource for breeding, gene discovery, conservation and evolutionary genomics.

genomics↗

bioRxiv2020

Comparison of long read methods for sequencing and assembly of a plant genome

Sequencing technologies have advanced to the point where it is possible to generate high accuracy, haplotype resolved, chromosome scale assemblies. Several long read sequencing technologies are available on the market and a growing number of algorithms have been developed over the last years to assemble the reads generated by those technologies. When starting a new genome project, it is therefore challenging to select the most cost-effective sequencing technology as well as the most appropriate software for assembly and polishing. For this reason, it is important to benchmark different approaches applied to the same sample. Here, we report a comparison of three long read sequencing technologies applied to the de novo assembly of a plant genome, Macadamia jansenii. We have generated sequencing data using Pacific Biosciences (Sequel I), Oxford Nanopore Technologies (PromethION) and BGI (single-tube Long Fragment Read) technologies for the same sample. Several assemblers were benchmarked in the assembly of PacBio and Nanopore reads. Results obtained from combining long read technologies or short read and long read technologies are also presented. The assemblies were compared for contiguity, accuracy and completeness as well as sequencing costs and DNA material requirements. Overall, the three long read technologies produced highly contiguous and complete genome assemblies of Macadamia jansenii. At the time of sequencing, the cost associated with each method was significantly different but continuous improvements in technologies have resulted in greater accuracy, increased throughput and reduced costs. We propose updating this comparison regularly with reports on significant iterations of the sequencing technologies.

genomics↗