Complete chloroplast genome sequencing of ten wild Fragaria species in China provides evidence for phylogenetic evolution of Fragaria

Sun, Jian; Sun, Rui; Liu, Huabo; Liu, Chang; Li, Shuangtao; Zhao, Mizhen; Shennan, Carol; Li, Jiajun; Dong, Jing; Zhong, Chuanfei; Xue, Liyan; Gao, Yingxin; Wang, Guixia; Zhang, Yuntao

doi:10.1016/j.ygeno.2021.01.027

Cited by 29 publications

(40 citation statements)

References 65 publications

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“…The intron region showed the highest variable rate, followed by the SSC, LSC, protein-coding regions, and IR region with the having the smallest rate. Our results are consistent with the previous studies on the chloroplast genomes of many land plants [13,19,26]. The nucleotide diversity of noncoding regions was higher than that in coding regions, suggesting suitability of the noncoding regions in Aroideae for the molecular marker identi cation, this is consistent with previous research in angiosperm chloroplast genomes [26], Thirteen intergenic regions (speci cally trnS-trnG) with highest-level of divergences (Pi > 0.17) could be developed as speci c molecular markers for species identi cation [27].…”

Section: Discussionsupporting

confidence: 94%

“…With the development and application of high-throughput sequencing technologies in genome sequence, the high abundance of chloroplast DNA compared to nuclear DNA have made it relatively easy to obtain complete chloroplast genome sequence without prior puri cation of chloroplasts or its DNA [17]. Over 5000 complete chloroplast genomes sequences have been published from crop and other land plant genomes [18][19][20] that lead to the development of comprehensive and accurate molecular markers for taxonomic, phylogenetic purposes and conservation of many valuable traits.…”

Section: Introductionmentioning

confidence: 99%

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Complete Chloroplast Genome Sequences of Three Aroideae Species (Araceae): Lights into Selective Pressure, Marker Development and Phylogenetic Relationships

Liu

Ali³

et al. 2021

Preprint

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Background : Colocasia gigantea, Caladium bicolor and Xanthosoma sagittifolium are three worldwide famous ornamental and/or vegetable plants in the Araceae family, these species in the subfamily Aroideae are taxonomically perplexing due to shared interspecific morphological traits and variation.Result : This study, for the first time ever, assembled and analyzed complete chloroplast genomes of C. gigantea, C. bicolor and X. sagittifolium with genome sizes of 165,906 bp, 153,149 bp and 165,169 bp in length, respectively. The genomes were composed of conserved quadripartite circular structures with a total of 131 annotated genes, including 8 rRNA, 37 tRNA and 86 protein-coding genes. A comparison within Aroideae showed seven protein-coding genes (accD, ndhF, ndhK, rbcL, rpoC1, rpoC2 and matK) linked to environmental adaptation. Phylogenetic analysis confirmed a close relationship of C. gigantea with C. esculenta and S. colocasiifolia, and the C. bicolor with X. sagittifolium. Furthermore, three DNA barcodes (atpH-atpI + psaC-ndhE, atpH-atpI + trnS-trnG, atpH-atpI + psaC-ndhE + trnS-trnG) harbored highly variable regions to distinguish species in Aroideae subfamily.Conclusion : These results would be beneficial for species identification, phylogenetic relationship, genetic diversity, and potential of germplasm resources in Aroideae.

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Section: Discussionsupporting

confidence: 94%

Section: Introductionmentioning

confidence: 99%

Complete Chloroplast Genome Sequences of Three Aroideae Species (Araceae): Lights into Selective Pressure, Marker Development and Phylogenetic Relationships

Liu

Ali³

et al. 2021

Preprint

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“…They also explain why the pollen tubes of F. nilgerrensis are strongly restricted in the styles of F. viridis and F. mandshurica in incompatible interspecific hybridizations. Moreover, the phylogenetic evolution of Fragaria shows that F. nilgerrens has a distant relationship with F. viridis and F. mandshurica 73 . Thus, the influence of phylogenetic distance on the compatibility of interspecific hybrids cannot be ruled out.…”

Section: Discussionmentioning

confidence: 99%

Molecular characteristics of S-RNase alleles as the determinant of self-incompatibility in the style of Fragaria viridis

Chen

et al. 2021

Horticulture Research

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Strawberry (Fragaria spp.) is a member of the Rosoideae subfamily in the family Rosaceae. The self-incompatibility (SI) of some diploid species is a key agronomic trait that acts as a basic pollination barrier; however, the genetic mechanism underlying SI control in strawberry remains unclear. Two candidate S-RNases (Sa- and Sb-RNase) identified in the transcriptome of the styles of the self-incompatible Fragaria viridis 42 were confirmed to be SI determinants at the S locus following genotype identification and intraspecific hybridization using selfing progenies. Whole-genome collinearity and RNase T2 family analysis revealed that only an S locus exists in Fragaria; however, none of the compatible species contained S-RNase. Although the results of interspecific hybridization experiments showed that F. viridis (SI) styles could accept pollen from F. mandshurica (self-compatible), the reciprocal cross was incompatible. Sa and Sb-RNase contain large introns, and their noncoding sequences (promotors and introns) can be transcribed into long noncoding RNAs (lncRNAs). Overall, the genus Fragaria exhibits S-RNase-based gametophytic SI, and S-RNase loss occurs at the S locus of compatible germplasms. In addition, a type of SI-independent unilateral incompatibility exists between compatible and incompatible Fragaria species. Furthermore, the large introns and neighboring lncRNAs in S-RNase in Fragaria could offer clues about S-RNase expression strategies.

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“…The complete mitochondrial genome of F. orientalis reported in this study will improve our understanding of Fragaria evolution. China is among the most diverse centers of wild strawberry resources, with 14 wild species, including 9 diploid species and all 5 tetraploid species (Sun et al 2021). Fragaria orientalis is a wild tetraploid strawberry, that is distributed mainly in Heilongjiang, Jilin and Liaoning Provinces of Northeast China (The CAS Editorial Committee of the Flora of China 1985; Lei et al 2017).…”

Section: Mitogenome Announcementmentioning

confidence: 99%

The complete mitochondrial genome sequence of Fragaria orientalis (Rosaceae)

Liu

Sun

et al. 2021

Mitochondrial DNA Part B

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Complete chloroplast genome sequencing of ten wild Fragaria species in China provides evidence for phylogenetic evolution of Fragaria

Cited by 29 publications

References 65 publications

Complete Chloroplast Genome Sequences of Three Aroideae Species (Araceae): Lights into Selective Pressure, Marker Development and Phylogenetic Relationships

Complete Chloroplast Genome Sequences of Three Aroideae Species (Araceae): Lights into Selective Pressure, Marker Development and Phylogenetic Relationships

Molecular characteristics of S-RNase alleles as the determinant of self-incompatibility in the style of Fragaria viridis

The complete mitochondrial genome sequence of Fragaria orientalis (Rosaceae)

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