Table_4_Comparative Genomics and Phylogenetic Analysis Revealed the Chloroplast Genome Variation and Interspecific Relationships of Corylus (Betulaceae) Species.XLSX

Corylus L. is an economically and phylogenetically important genus in the family Betulaceae. Taxonomic and phylogenetic relationships of Corylus species have long been controversial for lack of effective molecular markers. In this study, the complete chloroplast (cp) genomes of six Corylus species were assembled and characterized using next-generation sequencing. We compared the genome features, repeat sequences, sequence divergence, and constructed the phylogenetic relationships of the six Corylus species. The results indicated that Corylus cp genomes were typical of the standard double-stranded DNA molecule, ranging from 160,445 base pairs (bp) (C. ferox var. thibetca) to 161,621 bp (C. yunnanensis) in length. Each genome contained a pair of inverted repeats (IRs), a large single-copy (LSC) region and a small single-copy (SSC) region. Each of the six cp genomes possessed 113 unique genes arranged in the same order, including 80 protein-coding, 29 tRNA, and 4 rRNA genes. C. yunnanensis contained the highest number of repeat sequences, and the richest SSRs in six cp genomes were A/T mononucleotides. Comparative analyses of six Corylus cp genomes revealed four hotspot regions (trnH-psbA, rpoB-trnC, trnF-ndhJ, and rpl32-trnL) that could be used as potential molecular markers. Phylogenetic analyses of the complete chloroplast genomes and 80 protein-coding genes exhibited nearly identical topologies that strongly supported the monophyly of Corylus and simultaneously revealed the generic relationships among Betulaceae. The availability of these genomes can offer valuable genetic information for further taxonomy, phylogeny, and species delimitation in Corylus or even Betulaceae plants.

榛属（Corylus L.）是桦木科（Betulaceae）中兼具经济价值与系统发育重要性的属。榛属物种的分类学与系统发育关系长期存在争议，究其原因在于缺乏有效的分子标记。本研究利用下一代测序技术，组装并表征了6个榛属物种的完整叶绿体（chloroplast, cp）基因组。我们对这6个榛属物种的基因组特征、重复序列、序列分化情况进行了比较分析，并构建了其系统发育关系。研究结果显示，榛属叶绿体基因组均为典型的标准双链DNA分子，基因组长度介于160445碱基对（base pair, bp）（藏刺榛C. ferox var. thibetca）至161621 bp（云南榛C. yunnanensis）之间。每个基因组均包含一对反向重复序列（inverted repeats, IRs）、一个大单拷贝区（large single-copy, LSC）和一个小单拷贝区（small single-copy, SSC）。6个叶绿体基因组均拥有113个排列顺序一致的独特基因，其中包括80个蛋白编码基因、29个转运RNA（transfer RNA, tRNA）基因以及4个核糖体RNA（ribosomal RNA, rRNA）基因。云南榛的重复序列数量最多，而6个叶绿体基因组中丰度最高的简单序列重复（simple sequence repeat, SSR）均为A/T型单核苷酸重复。对6个榛属叶绿体基因组的比较分析揭示了4个高变热点区域（trnH-psbA、rpoB-trnC、trnF-ndhJ和rpl32-trnL），这些区域可作为潜在的分子标记。基于完整叶绿体基因组和80个蛋白编码基因的系统发育分析得到了几乎一致的拓扑结构，该结构强烈支持榛属为单系群，同时阐明了桦木科各属间的系统发育关系。上述叶绿体基因组的公开可为榛属乃至桦木科植物的后续分类学、系统发育研究以及物种界定提供宝贵的遗传信息。