Galactic Phylogenetics

Phylogenetics is a widely used concept in evolutionary biology. It is the reconstruction of evolutionary history by building trees that represent branching patterns and sequences. These trees represent shared history, and it is our intention for this approach to be employed in the analysis of Galactic history. In Galactic archaeology the shared environment is the interstellar medium in which stars form and provides the basis for tree-building as a methodological tool. Using elemental abundances of solar-type stars as a proxy for DNA, we built in Jofre et al 2017 such an evolutionary tree to study the chemical evolution of the solar neighbourhood. In this proceeding we summarise these results and discuss future prospects.Comment: Contribution to IAU Symposium No. 334: Rediscovering our Galax

Additional file 1: Table S1. of Abundant RNA editing sites of chloroplast protein-coding genes in Ginkgo biloba and an evolutionary pattern analysis

Primer sequences for detecting RNA editing sites. (DOC 140 kb

Additional file 2: Table S2. of Abundant RNA editing sites of chloroplast protein-coding genes in Ginkgo biloba and an evolutionary pattern analysis

RNA editing sites of Ginkgo biloba chloroplast protein-coding genes. (XLSX 26 kb

Table_1_Genome-wide identification and expression profiles analysis of the authentic response regulator gene family in licorice.xlsx

IntroductionAs one of the traditional Chinese medicinal herbs that were most generally used, licorice attracts lots of interest due to its therapeutic potential. Authentic response regulators (ARRs) are key factors in cytokinin signal transduction and crucial for plant growth and stress response processes. Nevertheless, the characteristics and functions of the licorice ARR genes are still unknown.ResultsIn present study, a systematic genome-wide identification and expression analysis of the licorice ARR gene family were conducted and 51 ARR members were identified. Collinearity analysis revealed the significant roles of segmental duplications in the expansion of licorice ARR genes. The cis-acting elements associated with development, stress and phytohormone responses were identified, implying their pivotal roles in diverse regulatory processes. RNA-seq and qRT-PCR results suggested that A-type, but not B-type ARRs were induced by zeatin. Additionally, ARRs participated in diverse abiotic stresses and phytohormones responses. Yeast one-hybrid assay demonstrated that GuARR1, GuARR2, GuARR11, GuARR12, GuARR10-1, GuARR10-2 and GuARR14 were able to bind to the promoter of GuARR8-3, and GuARR1, GuARR12 bound to the GuARR8-1 promoter. GuARR1, GuARR2, GuARR11 and GuARR10-2 bound to the GuARR6-2 promoter as well as GuARR12 and GuARR10-2 bound to the GuARR6-1 promoter.DiscussionCollectively, these findings provide a basis for future ARR genes function investigations, shedding light on the potential medicinal properties and agricultural applications of licorice.</p

Table_3_Genome-wide identification and expression profiles analysis of the authentic response regulator gene family in licorice.xlsx

IntroductionAs one of the traditional Chinese medicinal herbs that were most generally used, licorice attracts lots of interest due to its therapeutic potential. Authentic response regulators (ARRs) are key factors in cytokinin signal transduction and crucial for plant growth and stress response processes. Nevertheless, the characteristics and functions of the licorice ARR genes are still unknown.ResultsIn present study, a systematic genome-wide identification and expression analysis of the licorice ARR gene family were conducted and 51 ARR members were identified. Collinearity analysis revealed the significant roles of segmental duplications in the expansion of licorice ARR genes. The cis-acting elements associated with development, stress and phytohormone responses were identified, implying their pivotal roles in diverse regulatory processes. RNA-seq and qRT-PCR results suggested that A-type, but not B-type ARRs were induced by zeatin. Additionally, ARRs participated in diverse abiotic stresses and phytohormones responses. Yeast one-hybrid assay demonstrated that GuARR1, GuARR2, GuARR11, GuARR12, GuARR10-1, GuARR10-2 and GuARR14 were able to bind to the promoter of GuARR8-3, and GuARR1, GuARR12 bound to the GuARR8-1 promoter. GuARR1, GuARR2, GuARR11 and GuARR10-2 bound to the GuARR6-2 promoter as well as GuARR12 and GuARR10-2 bound to the GuARR6-1 promoter.DiscussionCollectively, these findings provide a basis for future ARR genes function investigations, shedding light on the potential medicinal properties and agricultural applications of licorice.</p

Table_4_Genome-wide identification and expression profiles analysis of the authentic response regulator gene family in licorice.xlsx

IntroductionAs one of the traditional Chinese medicinal herbs that were most generally used, licorice attracts lots of interest due to its therapeutic potential. Authentic response regulators (ARRs) are key factors in cytokinin signal transduction and crucial for plant growth and stress response processes. Nevertheless, the characteristics and functions of the licorice ARR genes are still unknown.ResultsIn present study, a systematic genome-wide identification and expression analysis of the licorice ARR gene family were conducted and 51 ARR members were identified. Collinearity analysis revealed the significant roles of segmental duplications in the expansion of licorice ARR genes. The cis-acting elements associated with development, stress and phytohormone responses were identified, implying their pivotal roles in diverse regulatory processes. RNA-seq and qRT-PCR results suggested that A-type, but not B-type ARRs were induced by zeatin. Additionally, ARRs participated in diverse abiotic stresses and phytohormones responses. Yeast one-hybrid assay demonstrated that GuARR1, GuARR2, GuARR11, GuARR12, GuARR10-1, GuARR10-2 and GuARR14 were able to bind to the promoter of GuARR8-3, and GuARR1, GuARR12 bound to the GuARR8-1 promoter. GuARR1, GuARR2, GuARR11 and GuARR10-2 bound to the GuARR6-2 promoter as well as GuARR12 and GuARR10-2 bound to the GuARR6-1 promoter.DiscussionCollectively, these findings provide a basis for future ARR genes function investigations, shedding light on the potential medicinal properties and agricultural applications of licorice.</p

A Potential Role for CHH DNA Methylation in Cotton Fiber Growth Patterns

<div><p>DNA methylation controls many aspects of plant growth and development. Here, we report a novel annual growth potential change that may correlate with changes in levels of the major DNA demethylases and methyltransferases in cotton ovules harvested at different times of the year. The abundances of DNA demethylases, at both the mRNA and protein levels, increased significantly from February to August and decreased during the remainder of the 12-month period, with the opposite pattern observed for DNA methyltransferases. Over the course of one year, substantial changes in methylcytosine content was observed at certain CHH sites (H = A, C, or T) in the promoter regions of the <i>ETHYLENE RESPONSIVE FACTOR 6</i> (<i>ERF6</i>), <i>SUPPRESSION OF RVS 161 DELTA 4</i> (<i>SUR4</i>) and <i>3-KETOACYL-COA SYNTHASE 13</i> (<i>KCS13</i>), which regulate cotton fiber growth. Three independent techniques were used to confirm the annual fluctuations in DNA methylation. Furthermore, in homozygous RNAi lines specifically targeting REPRESSOR OF SILENCING 1 (ROS1, a conserved DNA demethylase domain), promotion of DNA methylation significantly reduced fiber growth during August.</p> </div

Table_5_Genome-wide identification and expression profiles analysis of the authentic response regulator gene family in licorice.xlsx

IntroductionAs one of the traditional Chinese medicinal herbs that were most generally used, licorice attracts lots of interest due to its therapeutic potential. Authentic response regulators (ARRs) are key factors in cytokinin signal transduction and crucial for plant growth and stress response processes. Nevertheless, the characteristics and functions of the licorice ARR genes are still unknown.ResultsIn present study, a systematic genome-wide identification and expression analysis of the licorice ARR gene family were conducted and 51 ARR members were identified. Collinearity analysis revealed the significant roles of segmental duplications in the expansion of licorice ARR genes. The cis-acting elements associated with development, stress and phytohormone responses were identified, implying their pivotal roles in diverse regulatory processes. RNA-seq and qRT-PCR results suggested that A-type, but not B-type ARRs were induced by zeatin. Additionally, ARRs participated in diverse abiotic stresses and phytohormones responses. Yeast one-hybrid assay demonstrated that GuARR1, GuARR2, GuARR11, GuARR12, GuARR10-1, GuARR10-2 and GuARR14 were able to bind to the promoter of GuARR8-3, and GuARR1, GuARR12 bound to the GuARR8-1 promoter. GuARR1, GuARR2, GuARR11 and GuARR10-2 bound to the GuARR6-2 promoter as well as GuARR12 and GuARR10-2 bound to the GuARR6-1 promoter.DiscussionCollectively, these findings provide a basis for future ARR genes function investigations, shedding light on the potential medicinal properties and agricultural applications of licorice.</p

Table_2_Genome-wide identification and expression profiles analysis of the authentic response regulator gene family in licorice.xlsx

IntroductionAs one of the traditional Chinese medicinal herbs that were most generally used, licorice attracts lots of interest due to its therapeutic potential. Authentic response regulators (ARRs) are key factors in cytokinin signal transduction and crucial for plant growth and stress response processes. Nevertheless, the characteristics and functions of the licorice ARR genes are still unknown.ResultsIn present study, a systematic genome-wide identification and expression analysis of the licorice ARR gene family were conducted and 51 ARR members were identified. Collinearity analysis revealed the significant roles of segmental duplications in the expansion of licorice ARR genes. The cis-acting elements associated with development, stress and phytohormone responses were identified, implying their pivotal roles in diverse regulatory processes. RNA-seq and qRT-PCR results suggested that A-type, but not B-type ARRs were induced by zeatin. Additionally, ARRs participated in diverse abiotic stresses and phytohormones responses. Yeast one-hybrid assay demonstrated that GuARR1, GuARR2, GuARR11, GuARR12, GuARR10-1, GuARR10-2 and GuARR14 were able to bind to the promoter of GuARR8-3, and GuARR1, GuARR12 bound to the GuARR8-1 promoter. GuARR1, GuARR2, GuARR11 and GuARR10-2 bound to the GuARR6-2 promoter as well as GuARR12 and GuARR10-2 bound to the GuARR6-1 promoter.DiscussionCollectively, these findings provide a basis for future ARR genes function investigations, shedding light on the potential medicinal properties and agricultural applications of licorice.</p

Methylation-sensitive endonuclease digested PCR and Southern analysis of <i>ERF6</i>, <i>SUR4</i>, and <i>KCS13</i> upstream regions over one year.

<p>(A) Methylation-sensitive endonuclease digested PCR amplification of <i>ERF6</i> upstream region. Top: schematic diagram of the identification of a methylation-sensitive <i>BstX</i>I digenstion site (CCANNNNNNTGG) at −275 bp of the <i>ERF6</i> promoter. The bold C indicates a CHH site with annual methylation pattern change, corresponding to the cytosine labelled with red triangles in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060547#pone-0060547-g003" target="_blank">Figure 3A</a>. Bottom: PCR amplification using genomic DNA with (+) or without (−) <i>BstX</i>I digestion. (B) Southern blot of genomic DNA harvested at different times of the year, first digested by a methylation non-sensitive endonuclease <i>Mbo</i>II (TCTTC) to obtain a full length fragment of 605 bp from −621 to −15 of <i>ERF6</i> upstream regions, then digested thoroughly with <i>BstX</i>I, and probed with the fragment from −263 to −21 nt. The signal intensities of the band of <i>BstX</i>I-cleaved 244 bp changed at different time-of-year (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060547#pone.0060547.s012" target="_blank">Table S8</a>), indicating the methlytion levels of this CHH site were different, consistent with the bisulfite sequencing data in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060547#pone-0060547-g003" target="_blank">Figure 3A</a> and methylation-sensitive endonuclease digested PCR results in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060547#pone-0060547-g004" target="_blank">Figure 4A</a>. The same methylation-sensitive endonuclease digested PCR experiments were performed for the upstream regions of <i>SUR4</i> (C) and <i>KCS13</i> (E), except the methylation-sensitive endonucleases used were <i>HinF</i>I and <i>Bsl</i>I, respectively. Further, the same methylation-sensitive endonuclease digested Southern experiments were performed for the upstream regions of <i>SUR4</i> (D) and <i>KCS13</i> (F), except the genomic DNA were first digested by <i>Bcl</i>I (TGATCA) and <i>NSi</i>I (ATGCAT), then digested by methylation-sensitive endonucleases <i>HinF</i>I (GANTC) and <i>Bsl</i>I (CCNNNNNNNGG), respectively. The signal intensities of <i>HinF</i>I- and <i>Bsl</i>I-cleaved 330 bp and 837 bp changed similarly (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060547#pone.0060547.s012" target="_blank">Table S8</a>).</p