Institut de Recherche pour le Développement, DYNADIV Group, France.
Ann Bot. 2011 Dec;108(8):1433-44. doi: 10.1093/aob/mcr191. Epub 2011 Aug 9.
Molecular phylogenetic studies of palms (Arecaceae) have not yet provided a fully resolved phylogeny of the family. There is a need to increase the current set of markers to resolve difficult groups such as the Neotropical subtribe Bactridinae (Arecoideae: Cocoseae). We propose the use of two single-copy nuclear genes as valuable tools for palm phylogenetics.
New primers were developed for the amplification of the AGAMOUS 1 (AG1) and PHYTOCHROME B (PHYB) genes. For the AGAMOUS gene, the paralogue 1 of Elaeis guineensis (EgAG1) was targeted. The region amplified contained coding sequences between the MIKC K and C MADS-box domains. For the PHYB gene, exon 1 (partial sequence) was first amplified in palm species using published degenerate primers for Poaceae, and then specific palm primers were designed. The two gene portions were sequenced in 22 species of palms representing all genera of Bactridinae, with emphasis on Astrocaryum and Hexopetion, the status of the latter genus still being debated.
The new primers designed allow consistent amplification and high-quality sequencing within the palm family. The two loci studied produced more variability than chloroplast loci and equally or less variability than PRK, RPBII and ITS nuclear markers. The phylogenetic structure obtained with AG1 and PHYB genes provides new insights into intergeneric relationships within the Bactridinae and the intrageneric structure of Astrocaryum. The Hexopetion clade was recovered as monophyletic with both markers and was weakly supported as sister to Astrocaryum sensu stricto in the combined analysis. The rare Astrocaryum minus formed a species complex with Astrocaryum gynacanthum. Moreover, both AG1 and PHYB contain a microsatellite that could have further uses in species delimitation and population genetics.
AG1 and PHYB provide additional phylogenetic information within the palm family, and should prove useful in combination with other genes to improve the resolution of palm phylogenies.
palms（Arecaceae）的分子系统发育研究尚未提供该科完全解决的系统发育。需要增加当前的标记集来解决困难的群体，如 Neotropical 亚族 Bactridinae（Arecoideae：Cocoseae）。我们建议使用两个单拷贝核基因作为 palm 系统发育学的有价值工具。
为扩增 AGAMOUS 1（AG1）和 PHYTOCHROME B（PHYB）基因开发了新引物。对于 AGAMOUS 基因，靶向 Elaeis guineensis（EgAG1）的 paralogue 1。扩增的区域包含 MIKC K 和 C MADS-box 结构域之间的编码序列。对于 PHYB 基因，首先使用已发表的 Poaceae 简并引物在 palm 物种中扩增外显子 1（部分序列），然后设计特定的 palm 引物。在代表 Bactridinae 所有属的 22 种 palm 物种中对这两个基因部分进行了测序，重点是 Astrocaryum 和 Hexopetion，后者的属地位仍存在争议。
设计的新引物允许在 palm 科内进行一致的扩增和高质量测序。研究的两个基因座产生的变异性比叶绿体基因座多，与 PRK、RPBII 和 ITS 核标记的变异性相等或更少。使用 AG1 和 PHYB 基因获得的系统发育结构为 Bactridinae 属间关系以及 Astrocaryum 属内结构提供了新的见解。Hexopetion 进化枝在两种标记物中均被回收为单系，在联合分析中与 Astrocaryum sensu stricto 弱支持为姐妹群。罕见的 Astrocaryum minus 与 Astrocaryum gynacanthum 形成了一个物种复合体。此外，AG1 和 PHYB 都包含一个微卫星，这可能在物种界定和种群遗传学中进一步使用。
AG1 和 PHYB 在 palm 科内提供了额外的系统发育信息，并且与其他基因结合使用应该有助于提高 palm 系统发育的分辨率。
