Supplemental material for Xue et al., 2018

<table><tr><td><strong>Supplementary Table 1: </strong><strong> </strong><strong> </strong><table> <tr> <td><p><strong>Integrated genetic and physical map of the VPM1 segment on chromosome 2AS</strong></p><strong> </strong><strong> </strong><table> <tr> <td><strong>Supplementary Table 2: </strong><table> <tr> <td><strong>Fifty monomorphic SNP markers on the 27.8 Mb -33.9 Mb region on 2AS in emmer wheat</strong></td> </tr> </table></td></tr></table></td></tr></table></td></tr></table

Chromosomal location and genetic effects of <i>QTsg.osu-3A</i> for seed germination.

<p>The QTLs were characterized at high temperature (HT) and normal temperature (NT) in years 2008, 2009, and 2010, when seed was harvested 15, 30, or 45 days. Germination rate was tested in the recombinant inbred lines (RILs) of the Jagger×2174 population. Molecular markers along the chromosome are placed as centimorgans on the horizontal axis. The horizontal dotted line represents a common threshold value of 2.5 LOD.</p

A PCR marker for <i>TaMFT-A1</i>.

<p>Primer MFT-A1F2 and MFT-A1R2 were used to amplify <i>TaMFT-A1</i> from Jagger (331 bp) and 2174 (319 bp). PCR products were directly run on a 1% agarose gel.</p

Specific amplification of <i>TaMFT-A1</i>.

<p>Primer MFT-F1M and MFT-A1R1 were used to amplify the complete <i>TaMFT-A1</i> from three nullisomic-tetrasomic (NT) Chinese Spring (CS) lines, N3AT3B (1), N3BT3A (2), N3DT3A (3), as well as Jagger (4) and 2174 (5).</p

Genetic effect of <i>TaMFT-A1</i> on germination rate.

<p>The germination rate was averaged from each of the Jagger allele (A) or the 2174 allele (B) in the population (n = 96) that were characterized at high temperature (HT) and normal temperature (NT) in 2009 (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073330#pone-0073330-g006" target="_blank">Fig. 6A</a>) and 2010 (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073330#pone-0073330-g006" target="_blank">Fig. 6B</a>), when seed was harvested 15, 30, 45, or 70 days. Bar indicates standard error.</p

A summary of genetic effects of <i>QTsg.osu-3A</i> on seed germination under various temperatures.

<p>A summary of genetic effects of <i>QTsg.osu-3A</i> on seed germination under various temperatures.</p

Image2_Uncovering rearrangements in the Tibetan antelope via population-derived genome refinement and comparative analysis with homologous species.JPEG

Introduction: The Tibetan antelope (Pantholops hodgsonii) is a remarkable mammal thriving in the extreme Qinghai-Tibet Plateau conditions. Despite the availability of its genome sequence, limitations in the scaffold-level assembly have hindered a comprehensive understanding of its genomics. Moreover, comparative analyses with other Bovidae species are lacking, along with insights into genome rearrangements in the Tibetan antelope.Methods: Addressing these gaps, we present a multifaceted approach by refining the Tibetan Antelope genome through linkage disequilibrium analysis with data from 15 newly sequenced samples.Results: The scaffold N50 of the refined reference is 3.2 Mbp, surpassing the previous version by 1.15-fold. Our annotation analysis resulted in 50,750 genes, encompassing 29,324 novel genes not previously study. Comparative analyses reveal 182 unique rearrangements within the scaffolds, contributing to our understanding of evolutionary dynamics and species-specific adaptations. Furthermore, by conducting detailed genomic comparisons and reconstructing rearrangements, we have successfully pioneered the reconstruction of the X-chromosome in the Tibetan antelope.Discussion: This effort enhances our comprehension of the genomic landscape of this species.</p

Table1_Uncovering rearrangements in the Tibetan antelope via population-derived genome refinement and comparative analysis with homologous species.XLSX

Introduction: The Tibetan antelope (Pantholops hodgsonii) is a remarkable mammal thriving in the extreme Qinghai-Tibet Plateau conditions. Despite the availability of its genome sequence, limitations in the scaffold-level assembly have hindered a comprehensive understanding of its genomics. Moreover, comparative analyses with other Bovidae species are lacking, along with insights into genome rearrangements in the Tibetan antelope.Methods: Addressing these gaps, we present a multifaceted approach by refining the Tibetan Antelope genome through linkage disequilibrium analysis with data from 15 newly sequenced samples.Results: The scaffold N50 of the refined reference is 3.2 Mbp, surpassing the previous version by 1.15-fold. Our annotation analysis resulted in 50,750 genes, encompassing 29,324 novel genes not previously study. Comparative analyses reveal 182 unique rearrangements within the scaffolds, contributing to our understanding of evolutionary dynamics and species-specific adaptations. Furthermore, by conducting detailed genomic comparisons and reconstructing rearrangements, we have successfully pioneered the reconstruction of the X-chromosome in the Tibetan antelope.Discussion: This effort enhances our comprehension of the genomic landscape of this species.</p

Image3_Uncovering rearrangements in the Tibetan antelope via population-derived genome refinement and comparative analysis with homologous species.JPEG

Introduction: The Tibetan antelope (Pantholops hodgsonii) is a remarkable mammal thriving in the extreme Qinghai-Tibet Plateau conditions. Despite the availability of its genome sequence, limitations in the scaffold-level assembly have hindered a comprehensive understanding of its genomics. Moreover, comparative analyses with other Bovidae species are lacking, along with insights into genome rearrangements in the Tibetan antelope.Methods: Addressing these gaps, we present a multifaceted approach by refining the Tibetan Antelope genome through linkage disequilibrium analysis with data from 15 newly sequenced samples.Results: The scaffold N50 of the refined reference is 3.2 Mbp, surpassing the previous version by 1.15-fold. Our annotation analysis resulted in 50,750 genes, encompassing 29,324 novel genes not previously study. Comparative analyses reveal 182 unique rearrangements within the scaffolds, contributing to our understanding of evolutionary dynamics and species-specific adaptations. Furthermore, by conducting detailed genomic comparisons and reconstructing rearrangements, we have successfully pioneered the reconstruction of the X-chromosome in the Tibetan antelope.Discussion: This effort enhances our comprehension of the genomic landscape of this species.</p

Table3_Uncovering rearrangements in the Tibetan antelope via population-derived genome refinement and comparative analysis with homologous species.xlsx

Introduction: The Tibetan antelope (Pantholops hodgsonii) is a remarkable mammal thriving in the extreme Qinghai-Tibet Plateau conditions. Despite the availability of its genome sequence, limitations in the scaffold-level assembly have hindered a comprehensive understanding of its genomics. Moreover, comparative analyses with other Bovidae species are lacking, along with insights into genome rearrangements in the Tibetan antelope.Methods: Addressing these gaps, we present a multifaceted approach by refining the Tibetan Antelope genome through linkage disequilibrium analysis with data from 15 newly sequenced samples.Results: The scaffold N50 of the refined reference is 3.2 Mbp, surpassing the previous version by 1.15-fold. Our annotation analysis resulted in 50,750 genes, encompassing 29,324 novel genes not previously study. Comparative analyses reveal 182 unique rearrangements within the scaffolds, contributing to our understanding of evolutionary dynamics and species-specific adaptations. Furthermore, by conducting detailed genomic comparisons and reconstructing rearrangements, we have successfully pioneered the reconstruction of the X-chromosome in the Tibetan antelope.Discussion: This effort enhances our comprehension of the genomic landscape of this species.</p