Table_1_Plant-insect interactions across the Triassic–Jurassic boundary in the Sichuan Basin, South China.xlsx

Plants and insects are the most diverse and ecologically important organisms in the terrestrial biosphere. Their interactions are also among the richest biotic relationships, and offer significant insights into the evolution of terrestrial ecosystem complexity through the geological record. This investigation of the late Rhaetian Xujiahe and the earliest Jurassic Zhenzhuchong floral assemblages provides the first data on foliar herbivory generated by terrestrial arthropods across the Triassic–Jurassic transition in the eastern Tethys (East Asia) region. The damage types from two fossil assemblages are collectively attributed to seven functional feeding and egg-laying categories (i.e., hole feeding, margin feeding, surface feeding, skeletonization, piercing and sucking, oviposition, and galling). Most feeding strategies are spread across the major plant groups and persist through the Triassic–Jurassic boundary, with the exception of skeletonization (a category of external foliage feeding), which was restricted to the latest Triassic within dipteridacean ferns. The survey reveals that the respective frequency and diversity of interactions between plants and insects prior to and following the end-Triassic mass extinction event are almost the same, despite a substantial turnover of floral components. This suggest that insect herbivores were largely able to transfer to alternative (but commonly related) plant groups during the dramatic floristic turnover and environmental changes at the end of the Triassic. Sporadic occurrences of foliar modifications, such as marginal cusps on pinnules of Pterophyllum and prominent ridges on the rachises of some ferns and bennettites are interpreted as adaptations for defense against insect herbivores. A few differences in taxonomic composition and herbivory representation between the latest Triassic Xujiahe flora and the earliest Jurassic Zhenzhuchong flora are more likely to be related to collection and preservational biases rather than reflecting palaeoecological changes. We encourage further investigations exploring the distribution of insect damage in fossil floras from other palaeolatitudinal zones and spanning other major extinction events to develop a better understanding of terrestrial ecosystem responses to major crises in Earth’s history.</p

Identifying the Genome-Wide Sequence Variations and Developing New Molecular Markers for Genetics Research by Re-Sequencing a Landrace Cultivar of Foxtail Millet

<div><p>Foxtail millet (<i>Setaria</i><i>italica</i>) is a drought-resistant, barren-tolerant grain crop and forage. Currently, it has become a new model plant for cereal crops and biofuel grasses. Although two reference genome sequences were released recently, comparative genomics research on foxtail millet is still in its infancy. Using the Solexa sequencing technology, we performed genome re-sequencing on one important foxtail millet Landrace, Shi-Li-Xiang (SLX). Compared with the two reference genome sequences, the following genetic variation patterns were identified: 762,082 SNPs, 26,802 insertion/deletion polymorphisms of 1 to 5 bp in length (indels), and 10,109 structural variations (SVs) between SLX and Yugu1 genomes; 915,434 SNPs, 28,546 indels and 12,968 SVs between SLX and Zhang gu genomes. Furthermore, based on the Yugu1 genome annotation, we found out that ~ 40% SNPs resided in genes containing NB-ARC domain, protein kinase or leucine-rich repeats, which had higher non-synonymous to synonymous SNPs ratios than average, suggesting that the diversification of plant disease resistance proteins might be caused by pathogen pressure. In addition, out of the polymorphisms identified between SLX and Yugu1, 465 SNPs and 146 SVs were validated with more than 90% accuracy, which could be used as DNA markers for whole-genome genotyping and marker-assisted breeding. Here, we also represented an example of fine mapping and identifying a <i>waxy</i> locus in SLX using these newly developed DNA markers. This work provided important information that will allow a deeper understanding of the foxtail millet genome and will be helpful for dissecting the genetic basis of important traits in foxtail millet.</p> </div

Annotation and distribution of non-synonymous and synonymous SNPs in SLX genome compared with Yugu1.

<p>The Pfam domains of foxtail millet genes with 30 or more nonsynonymous and synonymous SNPs were analyzed and listed. <i>x</i>² significance of the observed non-synonymous and synonymous SNPs for each Pfam group is <i>p-value</i> < 0.001. The Pfam genes are arranged according to the ratios of nonsynonymous to synonymous SNPs. The numbers in the red and green bars show the absolute numbers of the non-synonymous and synonymous SNPs in each Pfam domain, respectively.</p

Distribution of the length of insertions and deletions polymorphisms identified between SLX and Yugu1 genome.

<p>The <i>x</i>-axis shows the number of nucleotides of deletions (orange) and insertions (blue). The <i>y</i>-axis shows the number of deletions or insertions at each length.</p

Distribution of IDPs in the SLX genome aligned with Yugu1 reference genome.

<p>A, Numbers of IDPs with different sizes in the whole genome and the CDS regions. B, Number of genes that contain IDPs with different sizes.</p

Annotation of large-effect SNPs in SLX genome compared with Yugu1.

<p>The numbers in the bars show the absolute numbers of large-effect SNPs for selected groups of genes. All the gene families shown were significantly abundant in large-effect SNPs (<i>p-value</i> < 0.001).</p

The electrophoresis gel image of PCR amplification of 56 newly developed SVs markers in SLX and Yugu1 genomes.

<p>Based on SVs identified between SLX and Yugu1, we selected 8 DEL variations with 100- to 400-bp in length from each chromosome (1st to 9th excluding 4th and 7th) to develop new DNA markers. S represents SLX, Y represents Yugu1, M represents DL2000 molecular makers.</p

Classification of SLX reads mapped onto the Yugu1 and Zhang gu genomes, respectively.

<p>A, SLX aligned with Yugu1 genome. B, SLX aligned with Zhang gu genome. The total number of mapped reads is in the center circle. The numbers of pair-end and single-end reads mapped onto chromosome and unmapped reads are shown in the middle circle. The outer circle represents unique or multiple mapping on chromosomes.</p

Map-based cloning of <i>waxy-slx</i>.

<p>A, Waxy trait of SLX compared with the non-waxy type of Yugu1 by staining their seeds in the I₂/KI solution. B, A fine genetic map of the <i>waxy-slx</i> region on chromosome 4 by new developed SV markers. C, A <i>TSI2</i> transposable element insertion was found in the first intron of the <i>starch </i><i>synthase</i> gene (Si006103m).</p

Annotation of SNPs, InDels and SVs identified between SLX and Yugu1.

<p>SNPs, InDels and SVs were classified as genetic and intergenic, and locations within the gene models were annotated based on the annotations of Yugu1 reference genome. The numbers and some proportions of three polymorphism types in each class are shown.</p