中越石灰岩溶植物─報春苣苔屬與石山苣苔屬之葉綠體基因體

Abstract

分布於中國華南與北越石灰岩地區之苦苣苔科(Gesneriaceae)報春苣苔屬(Primulina)與石山苣苔屬(Petrocodon)，擁有特殊的生境偏好與豐富的多樣性，為當地喀斯特物種之代表類群。本研究採用基因體略讀(genome skimming)之定序策略，定序八個報春苣苔屬與兩個石山苣苔屬物種之低覆蓋率(coverage)全基因體資料，獲取在細胞中擁有高副本數(copy number)的葉綠體基因(plastome)、粒線體外顯子體(mitochondria exome)與細胞核核醣體DNA (nuclear ribosomal DNA)之序列，並分別進行親緣關係樹的重建。此法不需透過成本較高的高覆蓋率定序，仍可獲得大量資料，並能夠增加同時定序的樣本數量。此外，八個下載自基因銀行(GenBank)的苦苣苔科物種之完整葉綠體基因體亦被納入基因體比較與親緣關係分析。雖然不同胞器DNA所重建之親緣關係樹存在許多不一致之處，但根據完整葉綠體基因體重建之演化關係具有極高支持度，可作為報春苣苔屬與其近緣屬間演化歷史之骨幹架構。藉由加入其他物種之序列進行比較，可得知所有納入分析之葉綠體基因體於基因組成與基因體的結構上均相當保守。本研究亦藉由排列比對報春苣苔屬與石山苣苔屬之完整葉綠體基因體序列，辨識出數個高變異的基因體區段，可作為未來進行族群遺傳與親緣關係研究所需的高解析力分子標記。

Primulina and Petrocodon, two characteristic Gesneriaceae genera of the limestone flora in southern China and northern Vietnam, are featured by their exclusive habitat preference and remarkable diversity. The genome skimming strategy, which sequences genomic DNA in low coverage to recover the high copy portions and to increase the multiplex level of sequencing, was employed to obtain complete plastomes, mitochondrial exomes and nuclear ribosomal DNAs of eight Primulina and two Petrocodon species. Phylogenies based on the data from the three cell compartments were reconstructed and compared. Additional eight Gesneriad plastomes (including five Primulina spp.) accessed online were incorporated in the comparative and phylogenetic analyses. The newly sequenced plastomes are highly conserved in genome structures and gene contents. Although the phylogenies inferred from plastid, mitochondrial and nuclear data are incongruent, the well supported plastome phylogeny represents a backbone relationships of Primulina and its allies. The sequence divergence among plastomes of Primulina and Petrocodon were evaluated to identify variable regions which serve as potentially useful markers for systematic or population studies.