Widespread and Adaptive Alterations in Genome-Wide Gene Expression Associated with Ecological Divergence of Two<i>Oryza</i>Species

Guo, Jie; Liu, Rong; Huang, Lei; Zheng, Xiaoming; Liu, Pingli; Du, Yu-Su; Cai, Zhe; Zhou, Lian; XingHua, Wei; Zhang, Fu‐Min; Ge, Song

doi:10.1093/molbev/msv196

Cited by 28 publications

(70 citation statements)

References 99 publications

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“…Meanwhile, Illumina-based plastid sequencing has been proven to be a valid and cost-effective way to acquire the complete cp DNA. Many assembled cp DNA of non-model species also have been obtained and employed for the study of differential gene expression, genetic markers development [28], phylogenomics analysis [29], as well as for detecting selection and inferring adaptive evolution within and among angiosperm species [30,31]. …”

Section: Introductionmentioning

confidence: 99%

Comparative Analysis of the Complete Chloroplast Genome of Four Endangered Herbals of Notopterygium

Yang

Yue

Niu

et al. 2017

Genes

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Notopterygium H. de Boissieu (Apiaceae) is an endangered perennial herb endemic to China. A good knowledge of phylogenetic evolution and population genomics is conducive to the establishment of effective management and conservation strategies of the genus Notopterygium. In this study, the complete chloroplast (cp) genomes of four Notopterygium species (N. incisum C. C. Ting ex H. T. Chang, N. oviforme R. H. Shan, N. franchetii H. de Boissieu and N. forrestii H. Wolff) were assembled and characterized using next-generation sequencing. We investigated the gene organization, order, size and repeat sequences of the cp genome and constructed the phylogenetic relationships of Notopterygium species based on the chloroplast DNA and nuclear internal transcribed spacer (ITS) sequences. Comparative analysis of plastid genome showed that the cp DNA are the standard double-stranded molecule, ranging from 157,462 bp (N. oviforme) to 159,607 bp (N. forrestii) in length. The circular DNA each contained a large single-copy (LSC) region, a small single-copy (SSC) region, and a pair of inverted repeats (IRs). The cp DNA of four species contained 85 protein-coding genes, 37 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes, respectively. We determined the marked conservation of gene content and sequence evolutionary rate in the cp genome of four Notopterygium species. Three genes (psaI, psbI and rpoA) were possibly under positive selection among the four sampled species. Phylogenetic analysis showed that four Notopterygium species formed a monophyletic clade with high bootstrap support. However, the inconsistent interspecific relationships with the genus Notopterygium were identified between the cp DNA and ITS markers. The incomplete lineage sorting, convergence evolution or hybridization, gene infiltration and different sampling strategies among species may have caused the incongruence between the nuclear and cp DNA relationships. The present results suggested that Notopterygium species may have experienced a complex evolutionary history and speciation process.

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Section: Introductionmentioning

confidence: 99%

Comparative Analysis of the Complete Chloroplast Genome of Four Endangered Herbals of Notopterygium

Yang

Yue

Niu

et al. 2017

Genes

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“…In these evolutionary contexts, ecological niche modelling (ENM) has been widely used to identify the environmental niche divergence between closely related taxa (Kozak et al 2008;Loera et al 2012;Guo et al 2015;Qu et al 2015). By integrating molecular phylogeography data, ENM has been conducted to detect whether pairs of sister species are more ecologically divergent than random expectation and even to clarify the relationship between genetic differentiation and abiotic factors (Knouft et al 2006;Blair et al 2013;Zhang et al 2014).…”

Section: Introductionmentioning

confidence: 99%

Geographical or ecological divergence between the parapatric species Ephedra sinica and E. intermedia?

et al. 2016

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Understanding the factors that contribute to population genetic structures and ecological niche divergence is crucial for elucidating the biogeographical history and speciation of plants. To disentangle the present phylogeographical patterns and evolutionary history of two closely related parapatric species from Ephedra (Ephedra sinica and E. intermedia), we systematically profiled their population genetic structures, niche divergence and potential speciation processes based on sequence variation of four chloroplast DNA fragments and climate-based ecological niche modelling (ENM). Phylogenetic analyses suggested that E. sinica formed a monophyly which was nested in E. intermedia. The latter species formed two paraphyletic subclades, corresponding to Western and Eastern lineages. Furthermore, the phylogeographical analysis results indicated very significant inter-and intraspecies genetic differentiation, and BEAST inference suggested that E. sinica diverged from E. intermedia at 3.20 million years ago (Ma; 95 % HPD: 2.05-8.10 Ma), while the Western lineage of E. intermedia diverged much earlier at 6.10 Ma (95 % HPD: 4.10-11.82 Ma). In addition, niche identity tests performed using MaxEnt strongly supported the hypothesis that the two sister species had significantly diverged on their ecological niches. Isolation by geographical and environment distance (IBD and IBE) tests suggested that the overall divergence of the populations from the two species were more influenced by environmental factors. Our data provide new insight into the ecological speciation of Ephedra and also provides molecular evidence for the identification and genetic conservation of these important pharmaceutical plants.

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“…Moreover, little is known on the effect of stress as a selective agent on gene regulation. A report on rice demonstrated that regulatory divergence is associated with ecological speciation and adaptive alterations (Guo et al 2015).…”

Section: Introductionmentioning

confidence: 99%

“…(O. rufipogon and O. nivara;Guo et al 2015) and among species of Arabidopsis (A. lyrata,A. halleri and A. thaliana;He et al 2016).…”

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confidence: 99%

cis dominantly explains regulatory divergence between two indica rice genotypes; drought further enhances regulatory differences

Ereful

Liu

Kao

et al. 2019

Preprint

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Background. cis and/or trans regulatory divergence within or between related taxa on a genome-wide scale has been largely unexamined in crops, more so, the effect of stress on cis/trans architecture. In this study, the indica genotypes IR64, an elite drought-susceptible lowland variety, and Apo (IR55423-01 or NSIC RC9), a moderate drought-tolerant upland genotype together with their hybrid (IR64 × Apo) were exposed to non-and water-stress conditions. Evidence of cis and/or trans regulatory differences was tested between these two indica rice genotypes.Results. By sequencing (RNA-seq) the parents and their hybrid, we are able to map genes diverging in cis and/or trans factors between the two genotypes. Under non-stress conditions, cis dominantly explains (11.2%) regulatory differences, followed by trans (8.9%). Further analysis showed that water-limiting conditions largely affect trans and cis + trans factors.Between the two inbred lines, Apo appears to exhibit higher expression fold change of genes enriched in "response to stress" and "photosynthesis" under non-and water-stress conditions.On the molecular level, cis and/or trans regulatory divergence explains their genotypic differences and differential drought response.Conclusions. Parent-hybrid RNA-seq has the potential to identify genes diverging in cis and/or trans factors even between intra-sub-specifically related genotypes. By comparing cis/trans landscape under stressed and unstressed conditions, this approach has the ability to assess the impact of drought on gene expression. Computational analysis and association of several drought-yield QTL markers with cis-and/or trans-diverging genes provide converging evidences suggestive of a potential approach to identify trait-associated candidate genes using hybrids and their parents alone.3

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Widespread and Adaptive Alterations in Genome-Wide Gene Expression Associated with Ecological Divergence of TwoOryzaSpecies

Cited by 28 publications

References 99 publications

Comparative Analysis of the Complete Chloroplast Genome of Four Endangered Herbals of Notopterygium

Comparative Analysis of the Complete Chloroplast Genome of Four Endangered Herbals of Notopterygium

Geographical or ecological divergence between the parapatric species Ephedra sinica and E. intermedia?

cis dominantly explains regulatory divergence between two indica rice genotypes; drought further enhances regulatory differences

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