Revisiting the phylogeny of Melastomataceae in the era of genomics

被子植物科是世界上最具多样性的十大科之一。3500新世界和C。1600个旧世界物种Clausing和Renner（2001）唯一的全科分子系统发育处理是基于仅使用叶绿体DNA序列的桑格测序，仅包括54个（~1%）物种。这些为数不多的质体标记的变异水平是不令人满意的，甚至整个cp基因组的测序也没有显示出深入的系统发育洞察力，也没有在解决黑口菌分子树方面取得进展。该家族缺乏强大的和解决的基因组学，缺乏基因组学工具，阻碍了进化和生态学研究，尽管它显示了许多非常有趣的特征，例如蜂群授粉的显著优势，各种形式的蚂蚁-植物相互作用，生长形式的巨大多样性，是热带植被中普遍存在的一种成分，是研究热带植被演化的理想类群。近年来，几种对基因组的选定子集进行测序的基因组划分策略已经成为植物基因组学中的有力工具，通过利用大量序列数据来解决物种关系，并潜在地缓解了先前的植物遗传学问题，这些问题是由于通过扩大性状和基因树的数量来限制对少数基因的取样而导致的。在本项目中，我们选择了两种方法：（1）Hyb-Seq，它结合了低拷贝核基因的靶标富集和基因组略读，使用低覆盖率的鸟枪测序来组装高拷贝基因组靶标。使用最近发表的被子植物范围内的HybSeq探针与melastome定制探针一起，我们的目标是与我们的美国和巴西同事合作，生成一个全科的Mexicataceae系统发育树，所有这些同事目前都在该家族工作。虽然所有实验室将共享和使用相同的协议和探针集，我们的实验室将集中在旧世界melastomes和我们的合作伙伴在NW类群。我们的目标是采样C。代表所有OW属的350种，尽管特别关注Dissochaeteae。(2)HyRAD提高了基因座覆盖率，并允许从高度降解的DNA样本中测序直链淀粉基因座，从而打开了使用博物馆藏品的可能性。使用修改后的HyRAD协议，我们将产生长，信息丰富的基因座适合物种树计算在低分类水平。我们的目标是解决两个物种丰富的分支内Dissochaeteae，马达加斯加Medinilla（c。70种）和东南亚蔓生灌木分支（约。98种）作为案例研究。这两种分子工具以及基于基因组数据的骨干系统发育学将促进系统的分类学研究，并随后促进该科的进化和生态学研究。

Melastomataceae range among the ten most diverse angiosperm families in the world with c. 3500 New World and c. 1600 Old World species. The only family-wide molecular phylogenetic treatment by Clausing and Renner (2001), was based on Sanger sequencing using only chloroplast DNA sequences with only 54 (~1%) species included. The level of variation across these few sampled plastid markers is unsatisfactory, and even sequencing of whole cp genomes showed no deep phylogenetic insight and progress in resolving the molecular trees in melastomes. Lack of robust and resolved phylogenies and lack of phylogenomic tools in this family hampers evolutionary and ecological studies although it shows a number of highly interesting features e.g. the conspicuous predominance of buzz-pollination, various forms of ant-plant interactions, an enormous diversity of growth forms, and is an ubiquitous element of tropical vegetation which makes it an ideal group to study the evolution of tropical vegetation.Over the past few years, several genome-partitioning strategies to sequence selected subsets of the genome, have emerged as powerful tools in plant phylogenomics, resolving species relationships by making use of vast sequence data and potentially alleviating previous problems of phylogenetics that resulted from limitation of sampling few genes by expanding the number of characters and gene trees. In this project we have chosen two methods: (1) Hyb-Seq, which combines target enrichment of low-copy nuclear genes and genome skimming, the use of low-coverage shotgun sequencing to assemble high-copy genomic targets. Using the recently published angiosperm-wide probes for HybSeq together with melastome customized probes, our aim is to generate a family-wide phylogenetic tree of Melastomataceae in cooperation with our American and Brazilian colleagues, all currently working in the family. While all labs will share and use the same protocols and probe sets, our lab will concentrates on the Old World melastomes and our partners on the NW taxa. We aim to sample c. 350 species representing all OW genera, albeit with a special focus on Dissochaeteae. (2) HyRAD which improves loci coverage and allows sequencing of orthologous loci from highly degraded DNA samples, opening the possibility to use museum collections. Using a modified HyRAD-protocol we will generate long, informative loci suitable for species tree calculation at low taxonomic levels. We aim to resolve two species rich clades within Dissochaeteae, the Madagascan Medinilla (c. 70 spp.) and the South East Asian scrambling shrubs clade (ca. 98 spp.) as case studies. Both molecular tools as well as the backbone phylogeny based on genomic data will promote systematic, taxonomic studies and subsequently boost evolutionary and ecological research in the family.