Chromosome-level genome assembly of a parent species of widely cultivated azaleas

Fang, Yang; Nie, Shuai; Liu, Hui; Shi, Tian-Le; Tian, Xue; Zhou, Shanshan; Bao, Yu-Tao; Jia, Kai‐Hua; Guo, Jing‐Fang; Wang, Zhao; An, Na; Zhang, Rengang; Yun, Quanzheng; Wang, Xinzhu; Mannapperuma, Chanaka; Porth, Ilga; El‐Kassaby, Yousry A.; Street, Nathaniel R.; Wang, Xiaoru; Peer, Yves Van de; Mao, Jian‐Feng

doi:10.1038/s41467-020-18771-4

Cited by 120 publications

(157 citation statements)

References 73 publications

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“…The rest of the genes were classified as singletons (12%), dispersed (47%), proximal (5%), and tandem (15%). Higher synonymous-to-non-synonymous substitution rate ratios (Ka/Ks) were found for proximal duplicate gene pairs, suggesting an ongoing and continuous process for proximal duplications, stronger positive selection, and faster sequence divergence than genes produced by other duplication phenomena ( Figure 2B ), similar to what has been observed in other Ericales species ( Yang et al, 2020 ). Comparison of cranberry against its wild relative ( V. microcarpum ), kiwifruit, tetraploid blueberry, tomato, grape and carrot yielded 20,163 (38.03%), 31,127 (49.15%), 64,919 (45.94%), 20,815 (39.36%), 17,165 (16.84%), and 22,728 (42.33%) collinear genes, respectively.…”

Section: Resultssupporting

confidence: 79%

“…Here, we dated a whole genome duplication event in the Ericales lineage 61 Mya. This WGD event is shared among members of the Ericaceae and Actinidiaceae families as also suggested previously ( Soza et al, 2019 ; Wu et al, 2019 ; Yang et al, 2020 ). Many studies have documented the co-occurrence of WGDs during the K-Pg boundary, a period in which most plant lineages started to diversify considerably ( Van de Peer et al, 2017 ).…”

Section: Discussionsupporting

confidence: 83%

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Chromosome-Level Genome Assembly of the American Cranberry (Vaccinium macrocarpon Ait.) and Its Wild Relative Vaccinium microcarpum

Diaz‐Garcia

García-Ortega²,

González-Rodríguez³

et al. 2021

Front. Plant Sci.

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The American cranberry (Vaccinium macrocarpon Ait.) is an iconic North American fruit crop of great cultural and economic importance. Cranberry can be considered a fruit crop model due to its unique fruit nutrient composition, overlapping generations, recent domestication, both sexual and asexual reproduction modes, and the existence of cross-compatible wild species. Development of cranberry molecular resources started very recently; however, further genetic studies are now being limited by the lack of a high-quality genome assembly. Here, we report the first chromosome-scale genome assembly of cranberry, cultivar Stevens, and a draft genome of its close wild relative species Vaccinium microcarpum. More than 92% of the estimated cranberry genome size (492 Mb) was assembled into 12 chromosomes, which enabled gene model prediction and chromosome-level comparative genomics. Our analysis revealed two polyploidization events, the ancient γ-triplication, and a more recent whole genome duplication shared with other members of the Ericaeae, Theaceae and Actinidiaceae families approximately 61 Mya. Furthermore, comparative genomics within the Vaccinium genus suggested cranberry-V. microcarpum divergence occurred 4.5 Mya, following their divergence from blueberry 10.4 Mya, which agrees with morphological differences between these species and previously identified duplication events. Finally, we identified a cluster of subgroup-6 R2R3 MYB transcription factors within a genomic region spanning a large QTL for anthocyanin variation in cranberry fruit. Phylogenetic analysis suggested these genes likely act as anthocyanin biosynthesis regulators in cranberry. Undoubtedly, these new cranberry genomic resources will facilitate the dissection of the genetic mechanisms governing agronomic traits and further breeding efforts at the molecular level.

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Section: Resultssupporting

confidence: 79%

Section: Discussionsupporting

confidence: 83%

Chromosome-Level Genome Assembly of the American Cranberry (Vaccinium macrocarpon Ait.) and Its Wild Relative Vaccinium microcarpum

Diaz‐Garcia

García-Ortega²,

González-Rodríguez³

et al. 2021

Front. Plant Sci.

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“…For example, duplicated counts are often omitted from BUSCO reporting but these can be a useful indicator for the amount of redundancy that remains in the assembly especially for highly heterozygous assemblies where the retention of both alleles in an allegedly haploid representation of the genome can be substantial (Michael & VanBuren, 2020; Rhie, McCarthy, et al, 2020). Elevated levels of BUSCO duplicates may alternatively report a contribution of whole genome duplication to the lineage, as is particularly common in plant and teleost fish genomes (e.g., De‐Kayne et al, 2020; Yang et al, 2020). Tools such as the LTR Assembly Index (LAI) attempt to describe the completeness of the repetitive content of an assembly and are further useful quality metric, particularly in repeat‐rich genomes (Ou et al, 2018).…”

Section: Evaluating Assembliesmentioning

confidence: 99%

The changing face of genome assemblies: Guidance on achieving high‐quality reference genomes

Whibley

Kelley

Narum

2021

Molecular Ecology Resources

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The quality of genome assemblies has improved rapidly in recent years due to continual advances in sequencing technology, assembly approaches, and quality control. In the field of molecular ecology, this has led to the development of exceptional quality genome assemblies that will be important long‐term resources for broader studies into ecological, conservation, evolutionary, and population genomics of naturally occurring species. Moreover, the extent to which a single reference genome represents the diversity within a species varies: pan‐genomes will become increasingly important ecological genomics resources, particularly in systems found to have considerable presence‐absence variation in their functional content. Here, we highlight advances in technology that have raised the bar for genome assembly and provide guidance on standards to achieve exceptional quality reference genomes. Key recommendations include the following: (a) Genome assemblies should include long‐read sequencing except in rare cases where it is effectively impossible to acquire adequately preserved samples needed for high molecular weight DNA standards. (b) At least one scaffolding approach should be included with genome assembly such as Hi‐C or optical mapping. (c) Genome assemblies should be carefully evaluated, this may involve utilising short read data for genome polishing, error correction, k‐mer analyses, and estimating the percent of reads that map back to an assembly. Finally, a genome assembly is most valuable if all data and methods are made publicly available and the utility of a genome for further studies is verified through examples. While these recommendations are based on current technology, we anticipate that future advances will push the field further and the molecular ecology community should continue to adopt new approaches that attain the highest quality genome assemblies.

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“…Few studies have examined the molecular basis underlying the formation and accumulation of anthocyanin in wild species [16,17]. Based on these studies, three major associated factors have been proposed to be involved in anthocyanin accumulation, including transcription regulatory genes (MYB-bHLH-WD40 complex) that occur in the nucleus, structural genes (CHS, FLS, DFR, ANS) acting in the biosynthetic pathway, and transporter genes (GST) transferring anthocyanin from the cytosol into the vacuole [10,18,19]. The expression of these genes could also be affected by natural variation in sequences and cis-regulatory elements as well as epigenetic modifications (such as DNA methylation) in the promoter regions [18,20].…”

Section: Introductionmentioning

confidence: 99%

Differential expressions of anthocyanin synthesis genes underlie flower color divergence in a sympatric Rhododendron sanguineum complex

Möller

Luo

et al. 2021

BMC Plant Biol

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Background The Rhododendron sanguineum complex is endemic to alpine mountains of northwest Yunnan and southeast Tibet of China. Varieties in this complex exhibit distinct flower colors even at the bud stage. However, the underlying molecular regulations for the flower color variation have not been well characterized. Here, we investigated this via measuring flower reflectance profiles and comparative transcriptome analyses on three coexisting varieties of the R. sanguineum complex, with yellow flush pink, bright crimson, and deep blackish crimson flowers respectively. We compared the expression levels of differentially-expressed-genes (DEGs) of the anthocyanin / flavonoid biosynthesis pathway using RNA-seq and qRT-PCR data. We performed clustering analysis based on transcriptome-derived Single Nucleotide Polymorphisms (SNPs) data, and finally analyzed the promoter architecture of DEGs. Results Reflectance spectra of the three color morphs varied distinctively in the range between 400 and 700 nm, with distinct differences in saturation, brightness, hue, and saturation/hue ratio, an indirect measurement of anthocyanin content. We identified 15,164 orthogroups that were shared among the three varieties. The SNP clustering analysis indicated that the varieties were not monophyletic. A total of 40 paralogous genes encoding 12 enzymes contributed to the flower color polymorphism. These anthocyanin biosynthesis-related genes were associated with synthesis, modification and transportation properties (RsCHS, RsCHI, RsF3H, RsF3′H, RsFLS, RsANS, RsAT, RsOMT, RsGST), as well as genes involved in catabolism and degradation (RsBGLU, RsPER, RsCAD). Variations in sequence and cis-acting elements of these genes might correlate with the anthocyanin accumulation, thus may contribute to the divergence of flower color in the R. sanguineum complex. Conclusions Our results suggested that the varieties are very closely related and flower color variations in the R. sanguineum complex correlate tightly with the differential expression levels of genes involved in the anabolic and catabolic synthesis network of anthocyanin. Our study provides a scenario involving intricate relationships between genetic mechanisms for floral coloration accompanied by gene flow among the varieties that may represent an early case of pollinator-mediated incipient sympatric speciation.

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Chromosome-level genome assembly of a parent species of widely cultivated azaleas

Cited by 120 publications

References 73 publications

Chromosome-Level Genome Assembly of the American Cranberry (Vaccinium macrocarpon Ait.) and Its Wild Relative Vaccinium microcarpum

Chromosome-Level Genome Assembly of the American Cranberry (Vaccinium macrocarpon Ait.) and Its Wild Relative Vaccinium microcarpum

The changing face of genome assemblies: Guidance on achieving high‐quality reference genomes

Differential expressions of anthocyanin synthesis genes underlie flower color divergence in a sympatric Rhododendron sanguineum complex

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