Genome size evolution of the extant lycophytes and ferns.
Genome size evolution of the extant lycophytes and ferns.
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现存石松类和蕨类植物的基因组大小进化
DOI：
10.1016/j.pld.2021.11.007
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发表时间：
2022-03
期刊：
影响因子：
4.8
通讯作者：
Yan, Yue-Hong
中科院分区：
文献类型：
--
作者：
Wang, Fa-Guo;Wang, Ai-Hua;Bai, Cheng-Ke;Jin, Dong-Mei;Nie, Li-Yun;Harris, A. J.;Che, Le;Wang, Juan-Juan;Li, Shi-Yu;Xu, Lei;Shen, Hui;Gu, Yu-Feng;Shang, Hui;Duan, Lei;Zhang, Xian-Chun;Chen, Hong-Feng;Yan, Yue-Hong
蕨类植物和石松植物有非常大的基因组。然而，很少有人知道他们的基因组大小如何在蕨类植物谱系进化。为探讨蕨类植物染色体数目和基因组大小的起源和演化，采用流式细胞术对27科72属240种（255个样本）蕨类植物和石松植物的基因组进行了测定，其中228种（242个样本）为新报道。我们在系统发育框架内分析了基因组大小、孢子大小、染色体特征、孢子发生和生境类型偏好之间的相关性。我们还应用方差分析和多项逻辑回归分析栖息地类型和基因组大小的偏好。利用遗传学，我们进行了祖先的性格重建的栖息地类型和测试是否基因组大小的变化，同时在栖息地偏好的转变。我们发现，2C值具有较弱的系统发育信号，而染色体的碱基数（x）具有较强的系统发育信号。此外，我们的分析揭示了基因组大小和染色体性状之间的正相关性，表明染色体的碱基数（x），染色体的大小，和多倍化可能是主要的贡献者在蕨类植物和石松植物的基因组扩增。不同生境类型的基因组大小差异显着，并与生境类型显着相关;具体而言，多项逻辑回归表明，具有较大的2C值的物种更有可能是附生植物。陆地栖息地被推断为祖先现存的蕨类植物和石松，而过渡到其他栖息地类型发生的主要分支出现。栖息地类型的变化似乎伴随着基因组稳定期。基于这些结果，我们推断，生境类型的变化和多个全基因组复制有助于形成大型基因组的蕨类植物及其盟友在其进化历史。这是第一项利用大数据更全面地分析现存蕨类植物和石松植物基因组大小进化的研究。我们检测到强烈的系统发育信号的染色体的碱基数蕨类植物。基因组大小与染色体性状（x和2n）呈显著正相关。具有较大的2C值的物种更有可能是附生植物，陆地栖息地被推断为祖先现存的蕨类植物和石松。在蕨类植物和石松植物的进化历史中，发生了从陆生生境向其他生境类型的转变。
Ferns and lycophytes have remarkably large genomes. However, little is known about how their genome size evolved in fern lineages. To explore the origins and evolution of chromosome numbers and genome size in ferns, we used flow cytometry to measure the genomes of 240 species (255 samples) of extant ferns and lycophytes comprising 27 families and 72 genera, of which 228 species (242 samples) represent new reports. We analyzed correlations among genome size, spore size, chromosomal features, phylogeny, and habitat type preference within a phylogenetic framework. We also applied ANOVA and multinomial logistic regression analysis to preference of habitat type and genome size. Using the phylogeny, we conducted ancestral character reconstruction for habitat types and tested whether genome size changes simultaneously with shifts in habitat preference. We found that 2C values had weak phylogenetic signal, whereas the base number of chromosomes (x) had a strong phylogenetic signal. Furthermore, our analyses revealed a positive correlation between genome size and chromosome traits, indicating that the base number of chromosomes (x), chromosome size, and polyploidization may be primary contributors to genome expansion in ferns and lycophytes. Genome sizes in different habitat types varied significantly and were significantly correlated with habitat types; specifically, multinomial logistic regression indicated that species with larger 2C values were more likely to be epiphytes. Terrestrial habitat is inferred to be ancestral for both extant ferns and lycophytes, whereas transitions to other habitat types occurred as the major clades emerged. Shifts in habitat types appear be followed by periods of genomic stability. Based on these results, we inferred that habitat type changes and multiple whole-genome duplications have contributed to the formation of large genomes of ferns and their allies during their evolutionary history. This is the first study to use big data to more comprehensively analyze the evolution of genome sizes of extant ferns and lycophytes. We detected strong phylogenetic signal for the base number of chromosomes of ferns. Genome size and chromosome traits (x and 2n) are significantly positive. Species with larger 2C values are more likely to be epiphytes, and terrestrial habitat is inferred to be ancestral for extant ferns and lycophytes. Transitions from terrestrial habitat to other habitat types occurred during the evolutionary history of ferns and lycophytes.
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影响因子：
3.3
作者：
Baniaga AE;Arrigo N;Barker MS
通讯作者：
Barker MS
影响因子：
4.2
作者：
Dolezel, J;Bartos, J
通讯作者：
Bartos, J
影响因子：
4.2
作者：
Christenhusz, Maarten J. M.;Chase, Mark W.;Viruel, Juan
通讯作者：
Viruel, Juan
DOI：
10.1073/pnas.0901635106
发表时间：
2009-11-17
影响因子：
11.1
作者：
Ackerly, David
通讯作者：
Ackerly, David
影响因子：
9.4
作者：
Clark, James;Hidalgo, Oriane;Schneider, Harald
通讯作者：
Schneider, Harald