Phylogenomic analyses and chromosome ploidy identification reveal multiple cryptic species in Allium sikkimense complex (Amaryllidaceae).
Phylogenomic analyses and chromosome ploidy identification reveal multiple cryptic species in Allium sikkimense complex (Amaryllidaceae).
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DOI：
10.3389/fpls.2023.1268546
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发表时间：
2023
影响因子：
5.6
通讯作者：
Sun, Hang
中科院分区：
文献类型：
--
作者：
Huang, De-Qing;Ma, Xiang-Guang;Sun, Hang
关键词：
多倍体化是一个通常导致瞬时生殖隔离的过程，因此，被认为是物种丰富的横断山区（HM）的主要进化力量之一，但这一主题在该地区的研究仍然很少。锡金葱及其近缘种（约8种）组成了一个天然的二倍体-多倍体复合体，在HM及其邻近地区具有最高的多样性。核核糖体DNA（nrDNA），质体，转录组和倍性鉴定，通过染色体计数和流式细胞术相结合，重建在这个复杂的系统发育关系，并调查复杂的频率和多倍体的进化意义。质体组未能解决A. sikkimense复合体，并且基于nrDNA的系统发育树也具有有限的分辨率。然而，我们的研究揭示了一个很好解决的系统发育框架的物种在A。sikkimense complex使用来自转录组数据的1，000多个正向同源基因。以前承认的形态种A。锡金人是非单系的并且包括至少两个独立进化的谱系（即，隐种），每一个形成一个分支与不同的二倍体物种在这个复杂的。四倍体A. jichouense和四倍体A. sp. nov.在A.锡金种支持一种可能的萌芽物种形成（通过生态位趋异）。此外，我们的研究结果表明，在A。sikkimense复合体通常具有不同的倍性水平，表明多倍体是同域葱属物种生殖隔离的重要过程。系统发生网络分析表明，A. sikkimense复合体，考虑到网状事件，总是比简单的分叉树更好地拟合数据集。此外，内收或外露的花丝，长期以来一直被用来界定物种，是非常不可靠的分类，由于其广泛的平行和趋同的进化。
Polyploidization is a process that typically leads to instantaneous reproductive isolation and has, therefore, been considered as one of the major evolutionary forces in the species-rich Hengduan Mountains (HM), yet this topic remains poorly studied in the region. Allium sikkimense and its relatives (about eight species) compose a natural diploid–polyploid complex with the highest diversity in the HM and adjacent areas. A combination of nuclear ribosomal DNA (nrDNA), plastome, transcriptome, and ploidy identification through chromosome counting and flow cytometry is employed to reconstruct the phylogenetic relationships in this complex and to investigate the frequency and the evolutionary significance of polyploidy in the complex. The plastome failed to resolve the phylogenetic relationships of the different species in the A. sikkimense complex, and the phylogenetic tree based on nrDNA also has limited resolution. However, our study reveals a well-resolved phylogenetic framework for species in the A. sikkimense complex using more than 1,000 orthologous genes from the transcriptome data. Previously recognized morphospecies A. sikkimense are non-monophyletic and comprise at least two independently evolved lineages (i.e., cryptic species), each forming a clade with different diploid species in this complex. The embedded pattern of octoploid A. jichouense and tetraploid A. sp. nov. within different polyploid samples of A. sikkimense supports a possible scenario of budding speciation (via niche divergence). Furthermore, our results reveal that co-occurring species in the A. sikkimense complex usually have different ploidy levels, suggesting that polyploidy is an important process for reproductive isolation of sympatric Allium species. Phylogenetic network analyses suggested that the phylogenetic relationships of the A. sikkimense complex, allowing for reticulation events, always fit the dataset better than a simple bifurcating tree. In addition, the included or exserted filaments, which have long been used to delimit species, are highly unreliable taxonomically due to their extensive parallel and convergent evolution.
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DOI：
10.1093/bioinformatics/bts565
发表时间：
2012-12-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Fu L;Niu B;Zhu Z;Wu S;Li W
通讯作者：
Li W
系统转录组学揭示龙胆亚族（龙胆科）中存在广泛的基因重复
影响因子：
3.7
作者：
Chen, Chun-Lin;Zhang, Lei;Xi, Zhen-Xiang
通讯作者：
Xi, Zhen-Xiang
DOI：
10.1093/bioinformatics/btp348
发表时间：
2009-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Capella-Gutiérrez S;Silla-Martínez JM;Gabaldón T
通讯作者：
Gabaldón T
影响因子：
9.4
作者：
Cai, Liming;Xi, Zhenxiang;Davis, Charles C.
通讯作者：
Davis, Charles C.
影响因子：
3
作者：
Gagnon, Edeline;Hilgenhof, Rebecca;Orejuela, Andres;McDonnell, Angela;Sablok, Gaurav;Aubriot, Xavier;Giacomin, Leandro;Gouvea, Yuri;Bragionis, Thamyris;Stehmann, Joao Renato;Bohs, Lynn;Dodsworth, Steven;Martine, Christopher;Poczai, Peter;Knapp, Sandra;Sarkinen, Tiina
通讯作者：
Sarkinen, Tiina