Long-read sequence assembly of the firefly <i>Pyrocoelia pectoralis</i> genome

Fu, Xiaozhe; Li, Jingjing; Tian, Yu; Quan, Weipeng; Zhang, Shu; Liu, Qian; Liang, Fan; Zhu, Xiaopeng; Zhang, Liangsheng; Wang, Depeng; Hu, Jiang

doi:10.1093/gigascience/gix112

Cited by 45 publications

(43 citation statements)

References 49 publications

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“…However, the haploid Pinot noir reference genome does not represent the typical complexity of commercial wine-grape cultivars and the heterozygous Pinot noir sequence remains highly fragmented [16]. In recent years, the maturation of single molecule long-read sequencing technologies such as those developed by PacBio [17] and Oxford Nanopore [18], and the development of diploid-aware assemblers such as FALCON [19] and CANU [20] have given rise to many highly-contiguous genome assemblies, including a draft genome assembly for the grapevine variety Cabernet sauvignon [19,[21][22][23][24]. Furthermore, whole genome phasing at the assembly level is possible with assemblers such as FALCON Unzip [19], allowing both haplotypes of a diploid organism to be characterised.…”

Section: Introductionmentioning

confidence: 99%

Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay

et al. 2018

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Chardonnay is the basis of some of the world's most iconic wines and its success is underpinned by a historic program of clonal selection. There are numerous clones of Chardonnay available that exhibit differences in key viticultural and oenological traits that have arisen from the accumulation of somatic mutations during centuries of asexual propagation. However, the genetic variation that underlies these differences remains largely unknown. To address this knowledge gap, a high-quality, diploid-phased Chardonnay genome assembly was produced from single-molecule real time sequencing, and combined with re-sequencing data from 15 different Chardonnay clones. There were 1620 markers identified that distinguish the 15 clones. These markers were reliably used for clonal identification of independently sourced genomic material, as well as in identifying a potential genetic basis for some clonal phenotypic differences. The predicted parentage of the Chardonnay haplomes was elucidated by mapping sequence data from the predicted parents of Chardonnay (Gouais blanc and Pinot noir) against the Chardonnay reference genome. This enabled the detection of instances of heterosis, with differentially-expanded gene families being inherited from the parents of Chardonnay. Most surprisingly however, the patterns of nucleotide variation present in the Chardonnay genome indicate that Pinot noir and Gouais blanc share an extremely high degree of kinship that has resulted in the Chardonnay genome displaying characteristics that are indicative of inbreeding.

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Section: Introductionmentioning

confidence: 99%

Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay

et al. 2018

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“…However, the haploid Pinot noir reference genome does not fully represent the typical complexity of commercial wine-grape cultivars and the heterozygous Pinot noir sequence remains highly fragmented (16). In recent years, the maturation of single molecule long-read sequencing technology such as those developed by PacBio (17) and Oxford Nanopore (18), and the development of diploid-aware assemblers such as FALCON (19) and CANU (20) has given rise to many highly-contiguous genome assemblies, including a draft genome assembly for the grapevine variety Cabernet sauvignon (19, 21–24). Furthermore, whole genome phasing at the assembly level is possible with assemblers such as FALCON Unzip (19), allowing both haplotypes of a diploid organism to be characterised.…”

Section: Introductionmentioning

confidence: 99%

Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay

Roach

Johnson

Bohlmann

et al. 2018

Preprint

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21Chardonnay is the basis of some of the world's most iconic wines and its success is 22 phenotypic trait. We produced a high-quality genome assembly for Chardonnay, and using 47 re-sequencing data for 15 popular clones, were able to identify a large selection of markers 48 that are unique to at least one clone. We identified mutations that may confer phenotypic 49 effects, and were able to identify clones from material independently sourced from nurseries 50 and vineyards. The marker detection framework we describe for authenticity testing would 51 be applicable to other grapevine cultivars or even other agriculturally important woody-plant 52 crops that are vegetatively propagated such as fruit orchards. Finally, we show that the 53 Chardonnay genome contains extensive evidence for parental inbreeding, such that its 54 parents, Gouais blanc and Pinot noir, may even represent first-degree relatives. 55A total of 614 primary contigs (397 Mb) and 1502 haplotigs (305 Mb) were confidently placed 130 in chromosomal order using the PN40024 scaffold as a reference. To analyse the degree 131 and distribution of heterozygosity across the genome, read depth (from mapped RS II 132 subreads), heterozygous variant density (from mapped Illumina short-reads) and phasing 133 coverage (from contig alignments) was calculated for the assembly (Fig 1A). 134Chromosomes 2, 3, 7, 15, 17, and 18 contain runs of homozygosity greater than 500 kb 135 (intersect of lack of phasing coverage, double read-depth, low heterozygous variant density). 136There are a further 22.8 Mb that lacked phasing coverage, had low heterozygous variant 137 density, and median read-depth. These regions presumably result from either hemizygosity 138 of these genomic regions, or undetected allelic duplicates remaining in the primary contigs. 139

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“…Pairwise BLASTP (v. 2.6.0, e-value 0.00001) searches were done between proteins of Marronus and O. borbonicus and best reciprocal hits were extracted to estimate the median protein sequence identity between orthologous gene pairs. For further comparative genomic analyses, we obtained protein sequences for Nicrophorus vespilloides and Aethina tumida from the i5k website (https://i5k.nal.usda.gov/, accessed July, 12th 2019) 45 , Anoplophora glabripennis , Dendroctonus ponderosae , Tribolium castaneum from Ensembl Metazoa (release 44), Protaetia brevitarsis , Pyrocoelia pectoralis , Hycleus cichorii and Hycleus phaleratus from GigaDB [46][47][48] , Onthophagus taurus from the U.S. Department of Agriculture website (https://data.nal.usda.gov, accessed July, 12th 2019), Agrilus planipennis and Leptinotarsa decemlineata 49 from the ftp server of the Human Genome Sequencing Center of the Baylor College of Medicine (ftp://ftp.hgsc.bcm.tmc.edu/I5K-pilot/, accessed July, 12th 2019), and Hypothenemus hampei from the website of the NYU Center for Health Informatics and Bioinformatics (https://genome.med.nyu.edu/) 50 . In cases of multiple isoforms per gene, the sequence corresponding to the longest protein was taken for further analysis.…”

Section: Gene Annotation and Comparative Genomic Analysismentioning

confidence: 99%

Museum phylogenomics of extinctOryctesbeetles from the Mascarene Islands

Latorre

Herrmann

Paulsen³

et al. 2020

Preprint

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The evolution of island systems is characterized by processes that result in extreme morphological diversity, high endemism and high extinction rates. These dynamics can make phylogenetic reconstruction difficult, i.e. the extinct flightless Dodo from Mauritius was assigned to the family of doves only through DNA analysis of subfossils. Many insect species on islands have gone extinct through habitat loss, and face similar challenges to decipher their evolutionary history, however historical specimens have not yet been harnessed for phylogenomic reconstructions. Here, we employed historical museum specimens from the Mascarene Islands to generate the first whole-genome based phylogeny of three presumably extinct species of the rhinoceros beetle genus Oryctes . We compared their genomes with those of an extant Oryctes species from the island of Réunion, as well as a flightless Réunion-based species previously placed into the supposedly unrelated genus Marronus . We found that Marronus borbonicus belongs instead to the genus Oryctes and that the two Réunion-based species ( O. borbonicus and M. borbonicus ) are not sister taxa, suggesting two independent colonizations. The divergence time between them (<3Myr) overlaps with the volcanic formation of Réunion, likely indicating that M. borbonicus became flightless in situ . Our study showcases the power of genomes from insect museum specimens to address evolutionary questions in light of increasing extinction rates.

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Long-read sequence assembly of the firefly Pyrocoelia pectoralis genome

Cited by 45 publications

References 49 publications

Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay

Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay

Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay

Museum phylogenomics of extinctOryctesbeetles from the Mascarene Islands

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