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Screening Three Single-copy Nuclear Markers to Infer Population Divergence in Conandron ramondioides (Gesneriaceae)

篩選三個單一拷貝核分子標記分析苦苣苔(Conandron ramondioides)之族群分歧

Abstracts


Conandron ramondioides (Gesneriaceae) belongs to a monotypic genus and is endemic to East Asia, occurring in Japan, southeastern China, and Taiwan. However, the pattern of colonization of C. ramondioides across East Asia is unclear. Molecular markers are usually used to reconstruct the history of organism or population colonization. To infer the colonization and population dynamics of this monotypic species, we developed single-copy nuclear markers. Eleven low-copy markers were randomly chosen from previous studies to design primers to amplify homologues from C. ramondioides. Agarose gel electrophoresis, cloning techniques, and Sanger sequencing were used to select single-copy nuclear markers. Three primer pairs were selected and used to investigate the genetic diversity of 58 individuals from 18 populations using next generation sequencing techniques. The nucleotide diversity (π) of these three single-copy nuclear markers was 0.007-0.0105, which is higher than that obtained using cpDNA markers. This strategy is useful for the development of single-copy nuclear markers for species without available transcriptomic or genomic data.

Parallel abstracts


苦苣苔為東亞特有苦苣苔科單型屬物種,分布於中國東南、日本與臺灣。然而苦苣苔在東亞的拓殖過程為何並不清楚。分子標記常被用以重建物種或是族群的拓殖過程。因此本研究開發單一拷貝分子標記,以期能解析重建苦苣苔族群在東亞的拓殖歷史。透過篩選,三對單一拷貝核分子標記,包含nuclear binding protein G2P(ATG2)內含子片段1,GroES內含子片段1與LEAFY內含子1,因在洋菜膠上呈現單一條帶,被採用於後續族群層級分析。這三對引子用於擴增58個苦苣苔個體並以次世代定序(NGS)方式定序。計算這三組引子對擴增DNA序列的核苷酸多樣性指數(π)分別為ATG2 intron 1: 0.007; GroES intron 1: 0.0105; LEAFY intron 1: 0.007。上述核苷酸多樣性指數數值高於由同為東亞分布草本植物葉綠體分子標記所得的核苷酸多樣性指數。因此,應用這三個分子標記所得的遺傳訊息,應能比採用葉綠體分子標記更利於重建苦苣苔在東亞的拓殖過程。同時,這個開發單拷貝核分子標記的方法學,對於無轉錄體與基因體數據的物種,將非常有幫助。

References


Cheng, S.,Melkonian, M.,Smith, S. A.,Brockington, S.,Archibald, J. M.,Delaux, PM.,Wong, G. K. S.(2018).10KP: A Phylodiverse Genome Sequencing Plan.GigaScience.giy013.
Doyle, J. J.,Doyle, J. L.(1987).A rapid DNA isolation procedure for small quantities of fresh leaf tissue.Phytochem. Bull..19(1),11-15.
Edgar, R. C.(2004).MUSCLE: multiple sequence alignment with high accuracy and high throughput.Nucleic Acids Res..32(5),1792-7.
Hall, T. A.(1999).BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT.Nucleic Acids Symp. Ser..41,95-98.
Kokubugata, G.,Peng, C. I.(2004).Floral morphology and recognition of varieties in Conan-dron ramondioides (Gesneriaceae) from Japan and Taiwan.Edinb..61(1),21-30.

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