Genome analysis of Taraxacum kok-saghyz Rodin provides new insights into rubber biosynthesis

Lin, Tao; Xu, Xia; Ruan, Jue; Liu, Shizhong; Wu, Shigang; Shao, Xiaorong; Wang, Xiaobo; Gan, Lu; Qin, Bi; Yang, Yan; Cheng, Zhukuan; Yang, Su–Hua; Zhang, Zhonghua; Xiong, Guosheng; Huang, Sanwen; Yu, Hong; Li, Jiayang

doi:10.1093/nsr/nwx101

Cited by 94 publications

(116 citation statements)

References 34 publications

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“…In many species, there is no data on polymorphism. Nevertheless, the complete sequences of a diploid individual consist of two haploid genomes, which could provide information on polymorphism 30,[37][38][39][40][41] . If genomes of single individuals can be used in lieu of a polymorphism survey, then the database would expand greatly.…”

Section: Additional Source Of Empirical Data -Genomes From One Indivimentioning

confidence: 99%

Two decades of suspect evidence for adaptive DNA-sequence evolution – Less negative selection misconstrued as positive selection

Chen

Feng

et al. 2020

Preprint

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Evidence for biological adaptation is often obtained by studying DNA sequence evolution. Since the analyses are affected by both positive and negative selection, studies usually assume constant negative selection in the time span of interest. For this reason, hundreds of studies that conclude adaptive evolution might have reported false signals caused by relaxed negative selection. We test this suspicion two ways. First, we analyze the fluctuation in population size, N, during evolution. For example, the evolutionary rate in the primate phylogeny could vary by as much as 2000 fold due to the variation in N alone. Second, we measure the variation in negative selection directly by analyzing the polymorphism data from four taxa (Drosophila, Arabidopsis, primates, and birds, with 64 species in total). The strength of negative selection, as measured by the ratio of nonsynonymous/synonymous polymorphisms, fluctuates strongly and at multiple time scales. The two approaches suggest that the variation in the strength of negative selection may be responsible for the bulk of the reported adaptive genome evolution in the last two decades. This study corroborates the recent report 1 on the inconsistent patterns of adaptive genome evolution. Finally, we discuss the path forward in detecting adaptive sequence evolution.

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Section: Additional Source Of Empirical Data -Genomes From One Indivimentioning

confidence: 99%

Two decades of suspect evidence for adaptive DNA-sequence evolution – Less negative selection misconstrued as positive selection

Chen

Feng

et al. 2020

Preprint

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“…RNA‐Seq data obtained from latex, root, and leaf mRNA expression profiles and the recently published draft genome of T. koksaghyz (Lin et al., ) were screened for the presence of SQS and SQE cDNA sequences. One contig showed high similarity to known SQS sequences and was strongly expressed in T. koksaghyz latex.…”

Section: Resultsmentioning

confidence: 99%

“…We injected 0.5 ll of the extract using split modus (1:10) at an injector and interface temperature of 260°C. The (Lin et al, 2017) were screened for the presence of SQS and SQE cDNA sequences. One contig showed high similarity to known SQS sequences and was strongly expressed in T. koksaghyz latex.…”

Section: Chemical Analysismentioning

confidence: 99%

Functional characterization of squalene synthase and squalene epoxidase in Taraxacum koksaghyz

Unland

Pütter²,

Vorwerk³

et al. 2018

Plant Direct

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“…The other five pairs of species were from the order Rodentia (Mus musculus and Rattus norvegicus), the order Carnivora (Felis catus and Canis lupus familiaris), the order Artiodactyla (Bos taurus and Ovis aries), the class Aves (Geospiza fortis and Taeniopygia guttata), and the class Reptilia (Chelonia mydas and Chrysemys picta bellii). Additional technical details used here can also be found in Lin et al (Lin, et al 2018) and Wang et al .…”

Section: Multiple Alignment Datamentioning

confidence: 99%

Molecular evolution in small steps under prevailing negative selection – A nearly-universal rule of codon substitution

Chen¹,

Lan²,

Shen³

et al. 2019

Preprint

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The widely accepted view that evolution proceeds in small steps is based on two premises: i) negative selection acts strongly against large differences (Kimura 1983); and ii) positive selection favors small-step changes (Fisher 1930). The two premises are not biologically connected and should be evaluated separately.We now extend the approach of Tang et al. (2004) to codon evolution for the entire genome. Codon substitution rate is a function of the physico-chemical distance between amino acids (AAs), equated with the step size of evolution. This step size depends on a large number of physico-chemical properties as 46 of the 48 properties examined affect the rate. Between 9 pairs of closely-related species of plants, invertebrates and vertebrates, the evolutionary rate is indeed strongly and negatively correlated with the AA distance (Δ U , scaled to [0, 1]). While the analyses corroborate the published results that relied on partial genomes, there is an important difference: Δ U is strongly correlated with the evolutionary rate (R 2 > 0.8) only when the genes are under predominant negative selection. Nevertheless, since most genes in most taxa are strongly constrained by negative selection, Δ U would appear to be a nearly-universal measure of codon evolution. In conclusion, the driving force of the small-step evolution at the codon level is negative selection. The unanswered question of whether positive selection may, or may not, follow the small-step rule will be addressed in a companion study (Chen, et al. 2019).

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Genome analysis of Taraxacum kok-saghyz Rodin provides new insights into rubber biosynthesis

Cited by 94 publications

References 34 publications

Two decades of suspect evidence for adaptive DNA-sequence evolution – Less negative selection misconstrued as positive selection

Two decades of suspect evidence for adaptive DNA-sequence evolution – Less negative selection misconstrued as positive selection

Functional characterization of squalene synthase and squalene epoxidase in Taraxacum koksaghyz

Molecular evolution in small steps under prevailing negative selection – A nearly-universal rule of codon substitution

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