LTR retrotransposons in rice (, L.): recent burst amplifications followed by rapid DNA loss-0

<p><b>Copyright information:</b></p><p>Taken from "LTR retrotransposons in rice (, L.): recent burst amplifications followed by rapid DNA loss"</p><p>http://www.biomedcentral.com/1471-2164/8/218</p><p>BMC Genomics 2007;8():218-218.</p><p>Published online 6 Jul 2007</p><p>PMCID:PMC1940013.</p><p></p>proximately at the same time. Upon insertion, all the new copies are identical in sequence as well as the two LTRs of each copy, leading to a null divergence between copies (Div = 0) and between the two LTRs of each copy (Div= 0). Over time, all sequences evolve at the same rate, so both the divergence between two copies and the divergence between the two LTRs of one copy are equal at a given time. Hence, if the nucleotide divergence between a truncated copy and a copy with two LTRs ("2 LTRs" copy) is equal to the nucleotide divergence between the two LTRs of the "2 LTRs" copy, the two copies originated from the same burst of amplification and the insertion date estimated for the "2 LTRs" copy can be used as an approximation of the insertion date of the truncated one

LTR retrotransposons in rice (, L.): recent burst amplifications followed by rapid DNA loss-1

<p><b>Copyright information:</b></p><p>Taken from "LTR retrotransposons in rice (, L.): recent burst amplifications followed by rapid DNA loss"</p><p>http://www.biomedcentral.com/1471-2164/8/218</p><p>BMC Genomics 2007;8():218-218.</p><p>Published online 6 Jul 2007</p><p>PMCID:PMC1940013.</p><p></p>sponding to a LTR divergence of 0.01 (0.385 My). For complete copies, ("2 LTRs") this divergence corresponds to the divergence between the two LTRs. For truncated copies (Internal Region [IR], LTR, and LTR-Internal region [LTR-IR]), the divergence is derived from the "2 LTRs" copies (see Materials and Methods and Figure 1)

Additional file 2 of Detection of active transposable elements in Arabidopsis thaliana using Oxford Nanopore Sequencing technology

S3 text file. Genomic sequences of 10 unique loci used to estimate the genome coverage of sequence data. Sequences are given in fasta format. (TXT 40 kb

The mobilome-seq approach in plants.

<p>A schematic view of the main steps involved in the selection and amplification of the extrachromosomal circular molecules in plants. After DNA extraction, linear DNA molecules are digested and circular molecules are randomly amplified using rolling circle amplification. This DNA material is used for high-throughput sequencing. Mobilome-seq data analysis consists in characterizing the depth of coverage (DOC) of mapped reads and the presence of split reads (SRs) at TE loci and the detection of <i>de novo</i> assembled scaffolds corresponding to these TEs.</p

Mobilome-seq detection of <i>Tos17</i>, a known active retrotransposon in rice callus.

<p>(<b>A</b>) Abundance of reads mapping at TE-annotated loci in the <i>O</i>. <i>sativa</i> WT callus mobilome-seq library. Each dot represents the normalized coverage per million mapped reads per all TE-containing 100bp windows obtained after aligning the sequenced reads on the <i>O</i>. <i>sativa</i> reference genome. Green dots indicate the windows corresponding to annotated <i>Tos17</i> genomic loci. (<b>B</b>) Detail of the depth of coverage of total mapped reads (DOC) and split reads (SRs) abundance of the <i>O</i>. <i>sativa</i> WT callus and leaf mobilome-seq library at the <i>Tos17</i> locus on chromosome 7 (<i>green bar</i>). Legend as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006630#pgen.1006630.g002" target="_blank">Fig 2C</a>. (<b>C</b>) Detection of circular forms of <i>Tos17</i> using inverse PCR with primers localization depicted on the right (<i>black bar</i>: <i>Tos17</i> element, <i>arrows</i>: PCR primers, <i>grey boxes</i>: LTRs). Upper gel: PCR amplification of <i>Tos17</i> circles, middle gel: control PCR for <i>Tos17</i> detection, lower gel: PCR using <i>eEF1α</i> primers as loading control. (<b>D</b>) Dotter alignment of the scaffold #29 obtained after <i>de novo</i> assembly of callus mobilome-seq library and <i>Tos17</i>.</p

Mobilome-seq detection of a novel active retrotransposon in rice seeds.

<p>(<b>A</b>) Genome-wide analysis of mobilome-seq data identifies the <i>PopRice</i> retrotransposon family as the most represented active family in WT rice seeds. Legend as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006630#pgen.1006630.g003" target="_blank">Fig 3A</a>. Pink dots indicate the windows corresponding to <i>Osr4</i> and <i>PopRice</i> loci. (<b>B</b>) Detail of the depth of coverage of total mapped reads and split reads abundance of the <i>O</i>. <i>sativa</i> WT seeds mobilome-seq library at the <i>PopRice</i> locus on chromosome 2 (<i>pink bar</i>) for callus and leaf mobilome-seq data. Legend as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006630#pgen.1006630.g002" target="_blank">Fig 2C</a>. (<b>C</b>) Phylogenic tree showing that <i>PopRice</i> is a distinct subfamily of <i>Osr4</i> LTR-RT. The relative DOC calculated from two biological replicates in WT seed mobilome-seq data is indicated as a heatmap. (<b>D</b>) Dotter alignment of the scaffold #17 obtained after <i>de novo</i> assembly of WT seed mobilome-seq library and a <i>PopRice</i> element.</p

<i>PopRice</i> retrotransposons produce extrachromosomal DNA during seed development in wild type rice.

<p>(<b>A</b>) Southern blot experiment using non-digested genomic DNA extracted from WT rice leaves and seeds at different stages as indicated and detected with a <i>PopRice</i> specific probe (<i>gDNA</i>: genomic DNA, <i>ecDNA</i>: extrachromosomal DNA). The GelRed gel picture is shown as a loading control. (<b>B</b>) Southern blot experiment using non-digested genomic DNA extracted from dissected rice seed tissues as indicated and detected with a <i>PopRice</i> specific probe. Legend as in A. (<b>C</b>) Detection of <i>PopRice</i> circular forms using inverse PCR with primers localization depicted on the right (<i>black bar</i>: <i>PopRice</i> element, <i>arrows</i>: PCR primers, <i>grey boxes</i>: LTRs). Upper gel: PCR amplification of <i>PopRice</i> circles, middle gel: control PCR for <i>PopRice</i> detection, lower gel: PCR using <i>eEF1α</i> primers as control. (<b>D</b>) qRT-PCR analysis of <i>PopRice</i> and <i>Osr4</i> transcripts in WT rice leaves, flowers and mature seeds. Two pairs of primers were used: <i>PopRice</i> specific primers (top) and primers specific for the whole <i>Osr4</i> family (including <i>PopRice</i>) (bottom). The relative expression levels were calculated using <i>eIF-5a</i> as a reference, error bars indicate technical replicates, two biological replicates are shown for each tissue.</p

Table_2_QTL Mapping Combined With Comparative Analyses Identified Candidate Genes for Reduced Shattering in Setaria italica.docx

<p>Setaria (L.) P. Beauv is a genus of grasses that belongs to the Poaceae (grass) family, subfamily Panicoideae. Two members of the Setaria genus, Setaria italica (foxtail millet) and S. viridis (green foxtail), have been studied extensively over the past few years as model species for C4-photosynthesis and to facilitate genome studies in complex Panicoid bioenergy grasses. We exploited the available genetic and genomic resources for S. italica and its wild progenitor, S. viridis, to study the genetic basis of seed shattering. Reduced shattering is a key trait that underwent positive selection during domestication. Phenotyping of F_2:3 and recombinant inbred line (RIL) populations generated from a cross between S. italica accession B100 and S. viridis accession A10 identified the presence of additive main effect quantitative trait loci (QTL) on chromosomes V and IX. As expected, enhanced seed shattering was contributed by the wild S. viridis. Comparative analyses pinpointed Sh1 and qSH1, two shattering genes previously identified in sorghum and rice, as potentially underlying the QTL on Setaria chromosomes IX and V, respectively. The Sh1 allele in S. italica was shown to carry a PIF/Harbinger MITE in exon 2, which gave rise to an alternatively spliced transcript that lacked exon 2. This MITE was universally present in S. italica accessions around the world and absent from the S. viridis germplasm tested, strongly suggesting a single origin of foxtail millet domestication. The qSH1 gene carried two MITEs in the 5′UTR. Presence of one or both MITEs was strongly associated with cultivated germplasm. If the MITE insertion(s) in qSH1 played a role in reducing shattering in S. italica accessions, selection for the variants likely occurred after the domestication of foxtail millet.</p

Image_4_QTL Mapping Combined With Comparative Analyses Identified Candidate Genes for Reduced Shattering in Setaria italica.jpg

<p>Setaria (L.) P. Beauv is a genus of grasses that belongs to the Poaceae (grass) family, subfamily Panicoideae. Two members of the Setaria genus, Setaria italica (foxtail millet) and S. viridis (green foxtail), have been studied extensively over the past few years as model species for C4-photosynthesis and to facilitate genome studies in complex Panicoid bioenergy grasses. We exploited the available genetic and genomic resources for S. italica and its wild progenitor, S. viridis, to study the genetic basis of seed shattering. Reduced shattering is a key trait that underwent positive selection during domestication. Phenotyping of F_2:3 and recombinant inbred line (RIL) populations generated from a cross between S. italica accession B100 and S. viridis accession A10 identified the presence of additive main effect quantitative trait loci (QTL) on chromosomes V and IX. As expected, enhanced seed shattering was contributed by the wild S. viridis. Comparative analyses pinpointed Sh1 and qSH1, two shattering genes previously identified in sorghum and rice, as potentially underlying the QTL on Setaria chromosomes IX and V, respectively. The Sh1 allele in S. italica was shown to carry a PIF/Harbinger MITE in exon 2, which gave rise to an alternatively spliced transcript that lacked exon 2. This MITE was universally present in S. italica accessions around the world and absent from the S. viridis germplasm tested, strongly suggesting a single origin of foxtail millet domestication. The qSH1 gene carried two MITEs in the 5′UTR. Presence of one or both MITEs was strongly associated with cultivated germplasm. If the MITE insertion(s) in qSH1 played a role in reducing shattering in S. italica accessions, selection for the variants likely occurred after the domestication of foxtail millet.</p

Image_5_QTL Mapping Combined With Comparative Analyses Identified Candidate Genes for Reduced Shattering in Setaria italica.PDF

<p>Setaria (L.) P. Beauv is a genus of grasses that belongs to the Poaceae (grass) family, subfamily Panicoideae. Two members of the Setaria genus, Setaria italica (foxtail millet) and S. viridis (green foxtail), have been studied extensively over the past few years as model species for C4-photosynthesis and to facilitate genome studies in complex Panicoid bioenergy grasses. We exploited the available genetic and genomic resources for S. italica and its wild progenitor, S. viridis, to study the genetic basis of seed shattering. Reduced shattering is a key trait that underwent positive selection during domestication. Phenotyping of F_2:3 and recombinant inbred line (RIL) populations generated from a cross between S. italica accession B100 and S. viridis accession A10 identified the presence of additive main effect quantitative trait loci (QTL) on chromosomes V and IX. As expected, enhanced seed shattering was contributed by the wild S. viridis. Comparative analyses pinpointed Sh1 and qSH1, two shattering genes previously identified in sorghum and rice, as potentially underlying the QTL on Setaria chromosomes IX and V, respectively. The Sh1 allele in S. italica was shown to carry a PIF/Harbinger MITE in exon 2, which gave rise to an alternatively spliced transcript that lacked exon 2. This MITE was universally present in S. italica accessions around the world and absent from the S. viridis germplasm tested, strongly suggesting a single origin of foxtail millet domestication. The qSH1 gene carried two MITEs in the 5′UTR. Presence of one or both MITEs was strongly associated with cultivated germplasm. If the MITE insertion(s) in qSH1 played a role in reducing shattering in S. italica accessions, selection for the variants likely occurred after the domestication of foxtail millet.</p