A whole genome assembly of <i>Leptospermum scoparium</i> (Myrtaceae) for mānuka research

Thrimawithana, Amali H.; Jones, Dan; Hilario, Elena; Grierson, Ella; Ngo, Hanh M.; Liachko, Ivan; Sullivan, Shawn; Bilton, Timothy P.; Jacobs, Jeanne M. E.; Bicknell, Ross; David, Charles N.; Deng, Cecilia; Nieuwenhuizen, Niels J.; López‐Girona, Elena; Tobias, Peri A; Morgan, E.R.; Perry, Nigel B.; Lewis, D. H.; Crowhurst, Ross N.; Davies, Kevin; Chagné, David; Schwinn, Kathy E.

doi:10.1080/01140671.2019.1657911

Cited by 37 publications

(37 citation statements)

References 74 publications

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“…We used the Hi‐C technology to reorder and anchor the total 99.44 % (441.27 Mb) of the genome onto 11 pseudochromosomes (Figure S2). The GC content of the assembled guava genome was 39.5%, which is similar to those of E. grandis (Myburg et al ., 2014) and L. scoparium (Thrimawithana et al ., 2019), the two most closely related species to guava with sequenced genomes.…”

Section: Resultsmentioning

confidence: 99%

“…These analyses predicted a total of 25 601 protein‐coding genes, representing 23.56% of the genome assembly (Table S7). This is a much smaller number of genes than in the sequenced genomes of the myrtaceous species, L. scoparium and E. grandis (Myburg et al ., 2014; Thrimawithana et al ., 2019). Among the 25 601 genes, 25 428 (99.3%) were functionally annotated (Table S8).…”

Section: Resultsmentioning

confidence: 99%

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A chromosome‐level genome assembly provides insights into ascorbic acid accumulation and fruit softening in guava (Psidium guajava)

Chen

Feng

Lin

et al. 2020

Plant Biotechnology Journal

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Summary Guava (Psidium guajava) is an important fleshy‐fruited tree of the Myrtaceae family that is widely cultivated in tropical and subtropical areas of the world and has attracted considerable attention for the richness of ascorbic acid in its fruits. However, studies on the evolution and genetic breeding potential of guava are hindered by the lack of a reference genome. Here, we present a chromosome‐level genomic assembly of guava using PacBio sequencing and Hi‐C technology. We found that the genome assembly size was 443.8 Mb with a contig N50 of ~15.8 Mb. We annotated a total of 25 601 genes and 193.2 Mb of repetitive sequences for this genome. Comparative genomic analysis revealed that guava has undergone a recent whole‐genome duplication (WGD) event shared by all species in Myrtaceae. In addition, through metabolic analysis, we determined that the L‐galactose pathway plays a major role in ascorbic acid biosynthesis in guava fruits. Moreover, the softening of fruits of guava may result from both starch and cell wall degradation according to analyses of gene expression profiles and positively selected genes. Our data provide a foundational resource to support molecular breeding of guava and represent new insights into the evolution of soft, fleshy fruits in Myrtaceae.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

A chromosome‐level genome assembly provides insights into ascorbic acid accumulation and fruit softening in guava (Psidium guajava)

Chen

Feng

Lin

et al. 2020

Plant Biotechnology Journal

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“…The A. psidii genome is particularly large compared with the average fungal genome, around 44.2 Mbp (Tavares et al 2014), and relative to its Myrtaceae hosts, around 300 - 650 Mbp (Thrimawithana et al 2019; Myburg et al 2014). Data based on flow cytometry determined the largest fungal genome at ∼3.6 Gbp (Egertová & Sochor 2017) and the largest known rust-type (Basidiomycota, Pucciniales) fungal genomes; Gymnosporangium confusum and Uromyces bidentis , at 893.2 Mbp and 2,489 Mbp, respectively (Ramos et al 2015).…”

Section: Discussionmentioning

confidence: 99%

Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements

Tobias

Schwessinger

Deng

et al. 2020

Preprint

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Austropuccinia psidii, originating in South America, is a globally invasive plant pathogen causing rust disease on Myrtaceae. Several biotypes are recognized with the most widely distributed pandemic strain spreading throughout the Asia-Pacific and Oceania regions within the last decade. Austropuccinia psidii has a broad host range (currently 480 myrtaceous species), making it a particularly dangerous plant pathogen. In the nine years since the pandemic biotype was first found in Australia in 2010, the pathogen has caused the near extinction of at least three species, the decline of at least one keystone species, and negatively affected commercial production of several Myrtaceae. To enable molecular and genomic studies into A. psidii pathogenicity, we assembled a highly contiguous genome for the pandemic biotype based on PacBio sequence data and scaffolding with Hi-C technology. With an estimated haploid genome size of just over 1 Gbp, it is the largest assembled fungal genome to date. We found the A. psidii genome to have a lower GC content (33.8 %), greatly expanded telomeric and intergenic regions and more repetitive regions (> 90 %) compared to other genomes of species in the Pucciniales, however numbers of predicted coding regions (18,875) are comparable. Most of the increase in genome size is caused by a recent expansion of transposable elements belonging to the Gypsy superfamily. Post-inoculation mRNA sequence capture from a susceptible host provides expression evidence for 10,613 predicted coding genes, including 210 of the 367 putative effectors. The completeness of the genome provides a greatly needed resource for strategic approaches to combat disease spread.3

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“…The A. psidii genome is particularly large compared with the average fungal genome, around 44.2 Mbp ( Tavares et al 2014 ), and relative to its Myrtaceae hosts, around 300–650 Mbp ( Myburg et al 2014 ; Thrimawithana et al 2019 ). Data based on flow cytometry determined the largest fungal genome at ∼3.6 Gbp ( Egertová and Sochor 2017 ) and the largest known rust-type (Basidiomycota, Pucciniales) fungal genomes; Gymnosporangium confusum and Uromyces bidentis , at 893.2 and 2489 Mbp, respectively ( Ramos et al 2015 ).…”

Section: Discussionmentioning

confidence: 99%

Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements

Tobias

Schwessinger

Deng

et al. 2020

G3 Genes|Genomes|Genetics

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Austropuccinia psidii, originating in South America, is a globally invasive fungal plant pathogen that causes rust disease on Myrtaceae. Several biotypes are recognized, with the most widely distributed pandemic biotype spreading throughout the Asia-Pacific and Oceania regions over the last decade. Austropuccinia psidii has a broad host range with more than 480 myrtaceous species. Since first detected in Australia in 2010, the pathogen has caused the near extinction of at least three species and negatively affected commercial production of several Myrtaceae. To enable molecular and evolutionary studies into A. psidii pathogenicity, we assembled a highly contiguous genome for the pandemic biotype. With an estimated haploid genome size of just over 1 Gb (gigabases), it is the largest assembled fungal genome to date. The genome has undergone massive expansion via distinct transposable element (TE) bursts. Over 90% of the genome is covered by TEs predominantly belonging to the Gypsy superfamily. These TE bursts have likely been followed by deamination events of methylated cytosines to silence the repetitive elements. This in turn led to the depletion of CpG sites in transposable elements and a very low overall GC content of 33.8%. Compared to other Pucciniales, the intergenic distances are increased by an order of magnitude indicating a general insertion of TEs between genes. Overall, we show how transposable elements shaped the genome evolution of A. psidii and provide a greatly needed resource for strategic approaches to combat disease spread.

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A whole genome assembly of Leptospermum scoparium (Myrtaceae) for mānuka research

Cited by 37 publications

References 74 publications

A chromosome‐level genome assembly provides insights into ascorbic acid accumulation and fruit softening in guava (Psidium guajava)

A chromosome‐level genome assembly provides insights into ascorbic acid accumulation and fruit softening in guava (Psidium guajava)

Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements

Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements

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