基因组时代的植物系统发育研究进展

系统发育研究是进化生物中的基本问题，也是其他众多生物学分支学科的基础问题，其核心在于研究不同生物类群间的亲缘关系与进化命运。利用分子数据研究生物之间的进化关系是系统发育研究的重要手段。随着测序技术的提升和测序成本的持续下降，系统发育研究由早期基于单基因或联合少数片段逐步发展到现阶段利用大规模基因组数据对个体、群体、物种以及更高水平的进化关系进行探讨。讨论了目前植物体内的3套基因组(叶绿体基因组、线粒体基因组与核基因组)在系统发育研究中的代表性成果，总结了植物不同基因组的特征及其在系统发育研究中的优势与局限，探讨了系统发育树构建的主要方法，并对未来研究进行了展望。目前，植物体内的3套基因组适用于不同阶元和类群的系统发育研究，不同基因组之间的遗传特性差异使其在系统发育研究中具备不同的优势和应用:① 叶绿体基因组结构相对简单，序列保守，不易重组，单亲遗传，是广泛应用于系统发育学和进化生物学等研究领域的理想分子数据资源；②植物线粒体基因组序列进化速率较慢，目前仅适用于早期植物和大尺度水平的系统发育研究；③核基因组为双亲遗传，可综合揭示双亲谱系及系统网状进化关系，在系统发育研究中具有巨大的应用潜力。不同建树方法适用于不同特征的数据集，在建树过程中应采用合理的方法避免长枝吸引和不完全谱系分选带来的影响。未来核基因组将成为系统发育研究的主流方向，其双亲遗传特性能够为物种形成过程中的杂交和基因组渗入等事件提供充分的见解。随着越来越多的类群系统位置被确定，物种形成和进化过程中的杂交、回交等双亲遗传，以及核质互作、多倍化、功能适应和趋同进化等问题将会成为系统发育研究的重点。表1参78

Advances in plant phylogeny in the genome era

Phylogeny is a basic issue in evolutionary biology and an important topic in other branches of biology as well, which focuses on the genetic relationship and evolutionary fate among various taxa. Using molecular data to investigate the evolutionary relationship between organism is an important means of phylogenetic research. Along with the development of sequencing technology and its decreasing cost, phylogenetic research has gradually developed from the early stage based on single gene or combined minority fragments to the present stage using massive genome data to study the evolutionary relationship among individuals, populations, and species. In this paper, the representative achievements of three sets of genomes (chloroplast genome, mitochondrial genome, and nuclear genome) in plant phylogenetic research are discussed. The characteristics of different plant genomes and their advantages and limitations in phylogenetic studies are summarized. The main methods of phylogenetic tree construction are explored and the future research is prospected. At present, the three sets of genomes in plants are suitable for phylogenetic studies of different order elements and taxa. The differences in genetic characteristics between different genomes have different advantages and applications in phylogenetic studies: (1) Chloroplast genome is relatively simple in structure, conservative in sequence, difficult to recombine, and uniparentally inherited. It is an ideal molecular data resource widely used in the fields of phylogeny and evolutionary biology. (2) The evolutionary rate of plant mitochondrial genome sequence is relatively slow, so it is only suitable for early plant and large-scale phylogenetic research. (3) The nuclear genome is biparental inheritance, which can comprehensively reveal the parental lineage and phylogenetic network evolutionary relationship, and has great application potential in phylogenetic research. Different tree construction methods are suitable for datasets with different characteristics, and reasonable methods should be adopted in the process of tree construction to avoid the effects of long-branch attraction and incomplete lineage sorting. In the future, nuclear genome will become the mainstream of phylogenetic research, and its biparental genetic characteristics can provide sufficient insights into hybridization and genomic introgression during speciation. With more taxon phylogenetic positions determined, biparental inheritance such as hybridization, backcross, nucleocytoplasmic interaction, polyploidy, functional adaptation, and convergent evolution during speciation and evolution will become the focus of phylogenetic research. Ch, 1 tab. 78 ref.]