Comparative chloroplast genomics of three species of Bulbophyllum section Cirrhopetalum (Orchidaceae), with an emphasis on the description of a new species from Eastern Himalaya.
Comparative chloroplast genomics of three species of Bulbophyllum section Cirrhopetalum (Orchidaceae), with an emphasis on the description of a new species from Eastern Himalaya.
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球兰科 Cirropetalum（兰科）三个物种的叶绿体基因组比较，重点是喜马拉雅东部一个新物种的描述
作者：
Li M;Tang L;Deng J;Tang H;Shao S;Xing Z;Luo Y
叶绿体基因组是一种有用的、信息丰富的分子标记，可用于物种测定和系统发育分析。球叶门是兰科植物中分类学最复杂的分类群之一。然而，球门植物的基因组特征尚不清楚。方法在比较形态学和基因组学分析的基础上，对喜马拉雅东部地区一新种球叶（Bulbophyllum pilopetalum）进行描述和图解。本研究利用叶绿体基因组序列和核糖体DNA （nrDNA）分析对球叶属新种进行了区分，并确定了其系统发育位置。利用球叶属植物15个完整叶绿体基因组的74个编码序列、33个球叶属植物的nrDNA序列和2个叶绿体DNA序列进行系统发育分析。结果该新种在营养形态和花形态上与平南布兰、白毛布兰和短柄布兰相似，但其卵形三角形背萼片无边缘纤毛。球叶植物叶绿体基因组全长151148 bp，包括一对25833 bp的反向重复序列（IRs）、86138 bp的大单拷贝区（LSC）和13300 bp的小单拷贝区（SSC）。叶绿体基因组包括108个独特的基因，编码75个蛋白质，30个trna和4个rrna。与其亲缘关系最近的两个种（平南白刺和白刺白刺）的cp基因组相比，该叶绿体基因组表现出很大的种间差异，并包含了几个新种特有的indel。质体树分析结果表明，毛毛莲与平南莲的亲缘关系最为密切。基于nrDNA和叶绿体DNA组合序列的系统进化树表明，Cirrhopetalum属单系植物，而pilopetalum属该植物。cp基因组数据有力地支持了该新种的分类地位。我们的研究强调了利用cp全基因组鉴定物种、阐明分类以及重建具有复杂分类问题的植物类群系统发育的重要性。
Background Chloroplast (cp) genomes are useful and informative molecular markers used for species determination and phylogenetic analysis. Bulbophyllum is one of the most taxonomically complex taxa in Orchidaceae. However, the genome characteristics of Bulbophyllum are poorly understood. Methods Based on comparative morphological and genomic analysis, a new species Bulbophyllum pilopetalum from eastern Himalaya belonging to section Cirrhopetalum is described and illustrated. This study used chloroplast genomic sequences and ribosomal DNA (nrDNA) analysis to distinguish the new Bulbophyllum species and determine its phylogenetic position. An additional phylogenetic analysis was conducted using 74 coding sequences from 15 complete chloroplast genomes from the genus Bulbophyllum, as well as nrDNA sequences and two chloroplast DNA sequences from 33 Bulbophyllun species. Results The new species is morphologically similar to B. pingnanense, B. albociliatum, and B. brevipedunculatum in vegetative and floral morphology, but it can be distinguished by its ovate-triangle dorsal sepal without a marginal ciliate. The chloroplast genome of the new Bulbophyllum species is 151,148 bp in length, and includes a pair of inverted repeats (IRs) of 25,833 bp, a large single-copy region (LSC) of 86,138 bp, and a small single-copy region (SSC) of 13,300 bp. The chloroplast genome includes 108 unique genes encoding 75 proteins, 30 tRNAs, and four rRNAs. Compared with the cp genomes of its two most closely-related species, B. pingnanense and B. albociliatum, this chloroplast genome exhibited great interspecific divergence and contained several Indels that were specific to the new species. The plastid tree showed that B. pilopetalum is most closely-related to B. pingnanense. The phylogenetic tree based on combined nrDNA and chloroplast DNA sequences indicated that section Cirrhopetalum was monophyletic and B. pilopetalum was a member of this section. Discussion The taxonomic status of the new species is strongly supported by cp genome data. Our study highlights the importance of using the complete cp genome to identify species, elucidate the taxonomy, and reconstruct the phylogeny of plant groups with complicated taxonomic problems.
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