JunctionViewer: customizable annotation software for repeat-rich genomic regions

<p>Abstract</p> <p>Background</p> <p>Repeat-rich regions such as centromeres receive less attention than their gene-rich euchromatic counterparts because the former are difficult to assemble and analyze. Our objectives were to 1) map all ten centromeres onto the maize genetic map and 2) characterize the sequence features of maize centromeres, each of which spans several megabases of highly repetitive DNA. Repetitive sequences can be mapped using special molecular markers that are based on PCR with primers designed from two unique "repeat junctions". Efficient screening of large amounts of maize genome sequence data for repeat junctions, as well as key centromere sequence features required the development of specific annotation software.</p> <p>Results</p> <p>We developed JunctionViewer to automate the process of identifying and differentiating closely related centromere repeats and repeat junctions, and to generate graphical displays of these and other features within centromeric sequences. JunctionViewer generates NCBI BLAST, WU-BLAST, cross_match and MUMmer alignments, and displays the optimal alignments and additional annotation data as concise graphical representations that can be viewed directly through the graphical interface or as PostScript^®output.</p> <p>This software enabled us to quickly characterize millions of nucleotides of newly sequenced DNA ranging in size from single reads to assembled BACs and megabase-sized pseudochromosome regions. It expedited the process of generating repeat junction markers that were subsequently used to anchor all 10 centromeres to the maize map. It also enabled us to efficiently identify key features in large genomic regions, providing insight into the arrangement and evolution of maize centromeric DNA.</p> <p>Conclusions</p> <p>JunctionViewer will be useful to scientists who wish to automatically generate concise graphical summaries of repeat sequences. It is particularly valuable for those needing to efficiently identify unique repeat junctions. The scalability and ability to customize homology search parameters for different classes of closely related repeat sequences make this software ideal for recurring annotation (e.g., genome projects that are in progress) of genomic regions that contain well-defined repeats, such as those in centromeres. Although originally customized for maize centromere sequence, we anticipate this software to facilitate the analysis of centromere and other repeat-rich regions in other organisms.</p

Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome

Recent comprehensive sequence analysis of the maize genome now permits detailed discovery and description of all transposable elements (TEs) in this complex nuclear environment. Reiteratively optimized structural and homology criteria were used in the computer-assisted search for retroelements, TEs that transpose by reverse transcription of an RNA intermediate, with the final results verified by manual inspection. Retroelements were found to occupy the majority (>75%) of the nuclear genome in maize inbred B73. Unprecedented genetic diversity was discovered in the long terminal repeat (LTR) retrotransposon class of retroelements, with >400 families (>350 newly discovered) contributing >31,000 intact elements. The two other classes of retroelements, SINEs (four families) and LINEs (at least 30 families), were observed to contribute 1,991 and ∼35,000 copies, respectively, or a combined ∼1% of the B73 nuclear genome. With regard to fully intact elements, median copy numbers for all retroelement families in maize was 2 because >250 LTR retrotransposon families contained only one or two intact members that could be detected in the B73 draft sequence. The majority, perhaps all, of the investigated retroelement families exhibited non-random dispersal across the maize genome, with LINEs, SINEs, and many low-copy-number LTR retrotransposons exhibiting a bias for accumulation in gene-rich regions. In contrast, most (but not all) medium- and high-copy-number LTR retrotransposons were found to preferentially accumulate in gene-poor regions like pericentromeric heterochromatin, while a few high-copy-number families exhibited the opposite bias. Regions of the genome with the highest LTR retrotransposon density contained the lowest LTR retrotransposon diversity. These results indicate that the maize genome provides a great number of different niches for the survival and procreation of a great variety of retroelements that have evolved to differentially occupy and exploit this genomic diversity

Conservation Status and Threat Assessments for North American Crop Wild Relatives

Conservation status and threat assessments evaluate species’ relative risks of extinction globally, regionally, nationally, or locally and estimate the degree to which populations of species are already safeguarded in existing conservation systems, with the aim of exposing the critical gaps in current conservation. Results of the assessments can therefore aid in directing limited conservation resources to the species and populations that are most at-risk. This chapter introduces the roles of conservation status and threat assessments in informing conservation priorities for crop wild relatives in North America and provides an overview of the current results for US taxa. Methods to assess the conservation status and to perform threat assessments for North American crop wild relatives are well developed via NatureServe and the International Union for Conservation of Nature (IUCN) Red List, and the essential infrastructure to perform these analyses is present, at least in Canada and the US. Current conservation assessments for North American wild relatives need updating but already reveal a landscape of multiple complex threats and major gaps in the ex situ and in situ conservation of prioritized species. Further resources and concerted efforts are needed to update conservation assessments and then to use the results to inform efforts to fill the critical gaps in conservation

The Effect of Deforestation on the Genetic Diversity and Structure in Acer Saccharum (marsh): Evidence for the Loss and Restructuring of Genetic Variation in a Natural System

The level and distribution of genetic diversity can be influenced by species life history traits and demographic factors, including perturbations that might produce population bottlenecks. Deforestation and forest fragmentation are common sources of population disturbance in contemporary populations of forest ecosystems. Although the genetic effects of forest fragmentation and deforestation have been examined by assessing levels of genetic variation in forest fragments that remain after logging, few considerations have been made of the populations that re-colonize once-cleared areas. Here we examine the effects of human-mediated population bottlenecks on the level and distribution of genetic diversity in natural populations of the long-lived forest tree species, Acer saccharum (sugar maple). We compared genetic variation and structure for populations of sugar maple found within old-growth forested area and in area that has re-colonized since logging. In this study the percent polymorphic loci and allelic richness estimates were reduced in the logged populations compared to old-growth populations. Jackknifed estimates of population genetic differentiation showed significantly higher differentiation among logged populations, with this result being consistently seen when individuals within populations were grouped according to diameter at breast height. The result of decreased genetic variation and higher levels of genetic structure among logged populations suggests that even one extensive bout of logging can alter the level and distribution of genetic variation in this forest tree species