利用基因组扫荡数据对附生姐妹属 Oreotrophe 和 Mukdenia（虎耳草科）进行叶绿体基因组分析和基因组资源开发。
Chloroplast genome analyses and genomic resource development for epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae), using genome skimming data.
机构信息
Key Laboratory of Plant Stress Biology, Laboratory of Plant Germplasm and Genetic Engineering, College of Life Sciences, Henan University, Kaifeng, 475000, China.
Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
出版信息
BMC Genomics. 2018 Apr 4;19(1):235. doi: 10.1186/s12864-018-4633-x.
BACKGROUND
Epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae) have an epilithic habitat (rocky slopes) and a parapatric distribution in East Asia, which makes them an ideal model for a more comprehensive understanding of the demographic and divergence history and the influence of climate changes in East Asia. However, the genetic background and resources for these two genera are scarce.
RESULTS
The complete chloroplast (cp) genomes of two Oresitrophe rupifraga and one Mukdenia rossii individuals were reconstructed and comparative analyses were conducted to examine the evolutionary pattern of chloroplast genomes in Saxifragaceae. The cp genomes ranged from 156,738 bp to 156,960 bp in length and had a typical quadripartite structure with a conserved genome arrangement. Comparative analysis revealed the intron of rpl2 has been lost in Heuchera parviflora, Tiarella polyphylla, M. rossii and O. rupifraga but presents in the reference genome of Penthorum chinense. Seven cp hotspot regions (trnH-psbA, trnR-atpA, atpI-rps2, rps2-rpoC2, petN-psbM, rps4-trnT and rpl33-rps18) were identified between Oresitrophe and Mukdenia, while four hotspots (trnQ-psbK, trnR-atpA, trnS-psbZ and rpl33-rps18) were identified within Oresitrophe. In addition, 24 polymorphic cpSSR loci were found between Oresitrophe and Mukdenia. Most importantly, we successfully developed 126 intergeneric polymorphic gSSR markers between Oresitrophe and Mukdenia, as well as 452 intrageneric ones within Oresitrophe. Twelve randomly selected intergeneric gSSRs have shown that these two genera exhibit a significant genetic structure.
CONCLUSIONS
In this study, we conducted genome skimming for Oresitrophe rupifraga and Mukdenia rossii. Using these data, we were able to not only assemble their complete chloroplast genomes, but also develop abundant genetic resources (cp hotspots, cpSSRs, polymorphic gSSRs). The genomic patterns and genetic resources presented here will contribute to further studies on population genetics, phylogeny and conservation biology in Saxifragaceae.
背景
附生姐妹属 Orestrohe 和 Mukdenia（虎耳草科）具有附生生境（石坡）和东亚的并系分布，这使它们成为更全面了解东亚种群和分化历史以及气候变化影响的理想模式。然而，这两个属的遗传背景和资源却很少。
结果
重建了两个 Orestrohe rupifraga 和一个 Mukdenia rossii 个体的完整叶绿体（cp）基因组，并进行了比较分析，以研究虎耳草科 cp 基因组的进化模式。cp 基因组的长度范围为 156738bp 至 156960bp，具有典型的四分体结构和保守的基因组排列。比较分析表明，Heuchera parviflora、Tiarella polyphylla、M. rossii 和 O. rupifraga 中的 rpl2 内含子丢失，但在 Penthorum chinense 的参考基因组中存在。在 Orestrohe 和 Mukdenia 之间鉴定出七个 cp 热点区域（trnH-psbA、trnR-atpA、atpI-rps2、rps2-rpoC2、petN-psbM、rps4-trnT 和 rpl33-rps18），而在 Orestrohe 内部鉴定出四个热点区域（trnQ-psbK、trnR-atpA、trnS-psbZ 和 rpl33-rps18）。此外，在 Orestrohe 和 Mukdenia 之间发现了 24 个多态性 cpSSR 位点。最重要的是，我们成功开发了 Orestrohe 和 Mukdenia 之间的 126 个种间多态性 gSSR 标记，以及 Orestrohe 内部的 452 个种内标记。随机选择的 12 个种间 gSSR 标记表明，这两个属具有显著的遗传结构。
结论
本研究对 Orestrohe rupifraga 和 Mukdenia rossii 进行了基因组浅测序。利用这些数据，我们不仅能够组装它们的完整叶绿体基因组，还能够开发丰富的遗传资源（cp 热点、cpSSR、多态性 gSSR）。这里呈现的基因组模式和遗传资源将有助于进一步研究虎耳草科的群体遗传学、系统发育和保护生物学。
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