Molecular footprints of selection effects and whole genome duplication (WGD) events in three blueberry species: detected by transcriptome dataset

Wang, Yunsheng; Nie, Fude; Shahid, Muhammad Qasim; Baloch, Faheem Shehzad

doi:10.1186/s12870-020-02461-w

Cited by 16 publications

(10 citation statements)

References 101 publications

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“…Our analysis agreed with results from a comparative genomics study in Rhododendron williamsianum and related species in the Ericaceae family that found two shared WGDs (the γ-triplication and Ac-β events) among cranberry (the Vm-α event found here), Camellia sinensis , and Rhododendron ( Soza et al, 2019 ). In relation to the evolutionary history of Vaccinium species, our molecular dating-based estimation for the divergence of cranberry- V. microcarpum ancestor and blueberry (10.4 Mya) agreed with a recent study ( Wang et al, 2020 ) dating the most recent polyploidization event in tetraploid blueberry (approximately 9 Mya) little after divergence.…”

Section: Resultssupporting

confidence: 86%

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: 86%

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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“…3 B ). Thus, 39.0% of the genes in the P. veris genome are present in two or more copies, similarly to other Ericales known to have experienced both the Ad -β and more recent WGDs ( Larson et al 2020 ; Wang et al 2020 ; supplementary fig. S16 , Supplementary Material online ).…”

Section: Resultsmentioning

confidence: 67%

Comparative Genomics Elucidates the Origin of a Supergene Controlling Floral Heteromorphism

Potente

Léveillé‐Bourret

Yousefi

et al. 2022

Molecular Biology and Evolution

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Supergenes are non-recombining genomic regions ensuring the co-inheritance of multiple, co-adapted genes. Despite the importance of supergenes in adaptation, little is known on how they originate. A classic example of supergene is the S locus controlling heterostyly, a floral heteromorphism occurring in 28 angiosperm families. In Primula, heterostyly is characterized by the co-occurrence of two complementary, self-incompatible floral morphs and is controlled by 5 genes clustered in the hemizygous, ca. 300-kbp S locus. Here we present the first chromosome-scale genome assembly of any heterostylous species, that of Primula veris (cowslip). By leveraging the high contiguity of the P. veris assembly and comparative genomic analyses, we demonstrated that the S-locus evolved via multiple, asynchronous gene duplications and independent gene translocations. Furthermore, we discovered a new whole-genome duplication in Ericales that is specific to the Primula lineage. We also propose a mechanism for the origin of S-locus hemizygosity via nonhomologous recombination involving the newly discovered two pairs of CFB genes flanking the S locus. Finally, we detected only weak signatures of degeneration in the S locus, as predicted for hemizygous supergenes. The present study provides a useful resource for future research addressing key questions on the evolution of supergenes in general and the S locus in particular: How do supergenes arise? What is the role of genome architecture in the evolution of complex adaptations? Is the molecular architecture of heterostyly supergenes across angiosperms similar to that of Primula?

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“…Noticeably, the VcSBP genes in the same group in the phylogenetic tree showed relatively low identity (8–48%) except the two segmental duplication pairs ( VcSPB7a and VcSBP7b , VcSBP14b , and VcSBP14c , Figures 1C , 2A ), suggesting that most VcSBP s might be single-copy genes with functional specificity. However, it was estimated that at least three rounds of whole-genome duplication occurred during the evolution of blueberry species ( Wang et al, 2020 ), which are supposed to facilitate the generation of multiple copy genes. It can be explained by at least two reasons: (1) it is still possible that the number of VcSBP genes might have been underestimated since the identification of SBP genes was conducted on the basis of available transcriptome data; (2) VcSBP s might belong to the duplication-resistant genes, which generally return to single-copy status through the duplication-resistant system or genetic drift after suffering duplication events ( Wang et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Comprehensive Analysis of the SBP Family in Blueberry and Their Regulatory Mechanism Controlling Chlorophyll Accumulation

et al. 2021

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SQUAMOSA Promoter Binding Protein (SBP) family genes act as central players to regulate plant growth and development with functional redundancy and specificity. Addressing the diversity of the SBP family in crops is of great significance to precisely utilize them to improve agronomic traits. Blueberry is an important economic berry crop. However, the SBP family has not been described in blueberry. In the present study, twenty VcSBP genes were identified through data mining against blueberry transcriptome databases. These VcSBPs could be clustered into eight groups, and the gene structures and motif compositions are divergent among the groups and similar within each group. The VcSBPs were differentially expressed in various tissues. Intriguingly, 10 VcSBPs were highly expressed at green fruit stages and dramatically decreased at the onset of fruit ripening, implying that they are important regulators during early fruit development. Computational analysis showed that 10 VcSBPs were targeted by miR156, and four of them were further verified by degradome sequencing. Moreover, their functional diversity was studied in Arabidopsis. Noticeably, three VcSBPs significantly increased chlorophyll accumulation, and qRT-PCR analysis indicated that VcSBP13a in Arabidopsis enhanced the expression of chlorophyll biosynthetic genes such as AtDVR, AtPORA, AtPORB, AtPORC, and AtCAO. Finally, the targets of VcSBPs were computationally identified in blueberry, and the Y1H assay showed that VcSBP13a could physically bind to the promoter region of the chlorophyll-associated gene VcLHCB1. Our findings provided an overall framework for individually understanding the characteristics and functions of the SBP family in blueberry.

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Molecular footprints of selection effects and whole genome duplication (WGD) events in three blueberry species: detected by transcriptome dataset

Cited by 16 publications

References 101 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

Comparative Genomics Elucidates the Origin of a Supergene Controlling Floral Heteromorphism

Comprehensive Analysis of the SBP Family in Blueberry and Their Regulatory Mechanism Controlling Chlorophyll Accumulation

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