蝴蝶蘭是全球花卉市場中重要的觀賞花卉之一，台灣阿嬤蝴蝶蘭(Phalaenopsis aphrodite, 2n= 2x= 38)是蝴蝶蘭重要的育種親本且其基因組(2.8 pg/ 2C)相對較小，因此是蝴蝶蘭屬全基因組定序的首選物種。蘭花尚未有整合遺傳、基因體與染色體結構資訊的分子細胞遺傳圖譜。本研究中，首先開發蝴蝶蘭粗絲期染色體的改良式染色體製備方法，台灣阿嬤蝴蝶蘭染色體於減數分裂粗絲期之解析度是有絲分裂中期染色體的20倍，並建立第一個台灣阿嬤蝴蝶蘭粗絲期染色體核型。進一步，透過螢光原位雜合技術將22個蝴蝶蘭遺傳連鎖群的基因體組裝序列，定位於19條粗絲期染色體上。此DNA標誌定位於染色體上的相對位置與連鎖圖譜及基因體組裝的結果一致，顯示已建立之遺傳連鎖圖譜與基因體組裝序列具有高度正確性。此外，這些已定位的DNA標誌可作為19條染色體專一性DNA標誌，加速染色體的辨識並協助將未定位的基因體組裝序列整合到已建立之分子細胞遺傳圖譜。最後，根據台灣阿嬤蝴蝶蘭基因組五個苯基苯乙烯酮合成酶基因之染色體位置、序列差異以及轉錄表現模式，推測染色體區段性複製後再發生串聯複製是造成此基因家族擴張的機制。本研究結果透過整合蝴蝶蘭遺傳、基因體與染色體資訊，為未來蘭花在染色體或比較基因體研究開創了不同的可能性並奠定重要的基礎。

Phalaenopsis orchid is one of the top ornamentals in global horticulture market. P. aphrodite (2n= 2x= 38) is an important parent in Phalaenopsis breeding and it is the specie of choice for whole genome sequencing owing to its relatively smaller genome size (2.8 pg/ 2C) in this genus. However, none of molecular cytogenetic map which integrates the genetic and genomic datasets to the chromosomal locations and structures was available in orchids. Fluorescence in situ hybridization (FISH) has been a reliable technique for mapping DNA markers on chromosomes. In this study, a modified drop method for pachytene chromosome preparation was first developed. Phalaenopsis meiotic pachytene chromosomes revealed up to 20 times higher resolution than their mitotic metaphase counterparts and the first pachytene-based karyotype of P. aphrodite was established. Second, the linkage group DNA markers were FISH mapped. Thus, the 22 Phalaenopsis linkage groups were successfully integrated with the 19 chromosomes of P. aphrodite. All the orders of the FISH signals were consistent to those revealed in the genome assembly and genetic linkage map, demonstrating the high quality of the physical and genetic maps. Furthermore, the anchored DNA markers were applied as chromosome-specific markers to facilitate chromosome identification and assisted to assign the unmapped scaffolds to the molecular cytogenetic map. Last, on the basis of chromosomal localizations, sequence divergences and transcriptomic expression profiles of the five CHS (chalcone synthase) genes, the expansion of the gene family occurred through segmental duplications followed by tandem duplications was proposed. The accomplishment of this study sets a solid foundation by integrating Phalaenopsis genetic, genomic and chromosomal datasets and opens the possibility for chromosome-scale comparative genomics in orchids.

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