Highly transferable microsatellite markers for the genera Lasiodiplodia and Neofusicoccum

Nagel, Jan Hendrik; Cruywagen, Elsie M.; Machua, Joseph; Wingfield, Michael J.; Slippers, Bernard

doi:10.1016/j.funeco.2019.100903

Cited by 6 publications

(7 citation statements)

References 62 publications

(97 reference statements)

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“…Lasiodiplodia pseudotheobromae (Botryosphaeriaceae, trials in the greenhouse and field suggested that this pathogen has a relatively high virulence to different Eucalyptus species or hybrids, compared to other species in Botryosphaeria and Neofusicoccum [7]. For this important pathogen, there are three isolates with publicly available genomic data in the NCBI database, CBS 116459 from Gemlina arborea [15], KET9 from Prunus persica [16] and BaA from Morinda officinalis [17] (DataFile 1; Table 1) [18]. These genome assemblies are fragmented and not suitable as reference genomes.…”

Section: Objectivementioning

confidence: 99%

“…An average of 2,081,811 ONT reads (up to 332 × coverage) and 49,479,273 Illumina clean reads (up to 192 × coverage) were generated in this study (DataFile 1; Table 1) [18]. The assembled draft genomes were about 43 Mb in size and with the highest N 50 value (5,817,267 bp) and the minimum contig numbers (8 contigs) among all the published L. pseudotheobromae genomes (DataFile 1; Table 1) [15][16][17]33]. For each of the five genomes, a perfect spectra graph performed by KAT program [34] was acquired, clearly showing a complete haplotype achieved.…”

Section: Data Descriptionmentioning

confidence: 99%

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High-quality genome resource of Lasiodiplodia pseudotheobromae associated with die-back on Eucalyptus trees

Lu,

Li,

Liu

2024

BMC Genom Data

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Objectives Lasiodiplodia pseudotheobromae is an important fungal pathogen associated with die-back, canker and shoot blight in many plant hosts with a wide geographic distribution. The aim of our study was to provide high-quality genome assemblies and sequence annotation resources of L. pseudotheobromae, to facilitate future studies on the systematics, population genetics and genomics of the fungal pathogen L. pseudotheobromae. Data description High-quality genomes of five L. pseudotheobromae isolates were sequenced based on Oxford Nanopore technology (ONT) and Illumina HiSeq sequencing platform. The total size of each assembly ranged from 43 Mb to 43.86 Mb and over 11,000 protein-coding genes were predicted from each genome. The proteins of predicted genes were annotated using multiple public databases, among the annotated protein-coding genes, more than 4,300 genes were predicted as potential virulence genes by the Pathogen Host Interactions (PHI) database. Moreover, the genome comparative analysis among L. pseudotheobromae and other closely related species revealed that 7,408 gene clusters were shared among them and 152 gene clusters unique to L. pseudotheobromae. This genome and associated datasets provided here will serve as a useful resource for further analyses of this fungal pathogen species.

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Section: Objectivementioning

confidence: 99%

Section: Data Descriptionmentioning

confidence: 99%

High-quality genome resource of Lasiodiplodia pseudotheobromae associated with die-back on Eucalyptus trees

Lu,

Li,

Liu

2024

BMC Genom Data

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“…Moreover, 60 primer pairs were developed and virtually amplified among genus Eucalyptus displayed interspecific polymorphism (30). Recently, 12 and 11 markers of Lasiodiplodia mahajangana and Neofusicoccum parvum tested for length variation and high transferability of the developed markers were observed (34).…”

Section: Transferability Of Common and Polymorphic Cpssrs In Genus Eucalyptusmentioning

confidence: 99%

“…Recently, common and unique SSRs have also been identified in several species (13,19,20). Moreover, transferability of SSRs was observed between Croton floribundus and Croton urucurana (Euphorbiaceae;31) and genus Lasiodiplodia and Neofusicoccum (34).…”

Section: Introductionmentioning

confidence: 99%

Length variation of chloroplast simple sequence repeats in the genus Eucalyptus L'Hér.

Kumar

Shanker

2020

Plant Sci. Today

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Eucalyptus L'Hér. is an economically important genus of plants with several environmental significances and great industrial advantages. To accelerate breeding and conservation studies, efforts on molecular breeding and molecular genetic analysis are underway in the genus Eucalyptus. Despite these efforts, no sufficient information is available about common, polymorphic and unique chloroplast simple sequence repeats (cpSSRs) in the genus Eucalyptus. . These repeats consist of 1-6 nucleotides and play important role in the development of molecular markers, genetic mapping and plant breeding. In the present study, a total of 920 cpSSRs were detected and length variation of cpSSRs analysed between each pair of species among 31 chloroplast genome sequences of the genus Eucalyptus. Additionally, cross species transferability of common and polymorphic cpSSRs were also observed. The common, unique and putative polymorphic cpSSRs analysed in this study can be used for species identification and genetic diversity studies of Eucalyptus.

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“…The faulty genotyping profiles could have resulted due to non-target 11 primer annealing. The increased phylogenetic distance between the source (big cats: genus Panthera) and target (Eurasian lynx: genus Lynx) species greatly reduces transferability of markers54 .…”

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confidence: 99%

Whole genome survey of big cats (Genus:Panthera) identifies novel microsatellites of utility in conservation genetic study

Hyun

Pandey

Kim

et al. 2020

Preprint

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AbstractBig cats (Genus: Panthera) are among the most threatened mammal groups of the world, owing to illegal transnational trade. Conservation genetic studies and effective curbs on poaching are important for the conservation of these charismatic apex predators. A limited number of microsatellite markers exists for Panthera species and researchers often cross-amplify domestic cat microsatellites to study these species. We conducted data mining of seven Panthera genome sequences to discover microsatellites for conservation genetic studies of four threatened big cat species. A total of 32 polymorphic microsatellite loci were identified in silico and tested with 99 big cat individuals and 7 Eurasian lynx. The developed markers were polymorphic in most of the tested species. We propose a set of 15 novel microsatellite markers for use in conservation genetics and wildlife forensic investigations of big cat species. Cumulatively, these markers have a high discriminatory power of one in a million for unrelated individuals and one in a thousand for siblings. Similar PCR conditions of these markers increase the prospects of achieving efficient multiplex PCR assays. This study is a pioneering attempt to synthesise genome wide microsatellite markers for big cats.

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Highly transferable microsatellite markers for the genera Lasiodiplodia and Neofusicoccum

Cited by 6 publications

References 62 publications

High-quality genome resource of Lasiodiplodia pseudotheobromae associated with die-back on Eucalyptus trees

High-quality genome resource of Lasiodiplodia pseudotheobromae associated with die-back on Eucalyptus trees

Length variation of chloroplast simple sequence repeats in the genus Eucalyptus L'Hér.

Whole genome survey of big cats (Genus:Panthera) identifies novel microsatellites of utility in conservation genetic study

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