Browsing by Author "Xing, Jinchuan"
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Item Targeted capture of phylogenetically informative ves SINE insertions in genus Myotis(2015) Platt, Roy N. (TTU); Zhang, Yuhua; Witherspoon, David J.; Xing, Jinchuan; Suh, Alexander; Keith, Megan S. (TTU); Jorde, Lynn B.; Stevens, Richard D. (TTU); Ray, David A. (TTU)Identification of retrotransposon insertions in nonmodel taxa can be technically challenging and costly. This has inhibited progress in understanding retrotransposon insertion dynamics outside of a fewwell-studied species. To address this problem,wehave extended a retrotransposon-based capture and sequence method (ME-Scan [mobile element scanning]) to identify insertions belonging to the Ves family of short interspersed elements (SINEs) across seven species of the bat genus Myotis. We identified between 120,000 and 143,000 SINE insertions in six taxa lacking a draft genomeby comparing to the M. lucifugus reference genome.Onaverage, eachVes insertion was sequenced to 129.6 × coverage. When mapped back to the M. lucifugus reference genome, all insertions were confidently assigned within a 10-bp window. Polymorphic Ves insertions were identified in each taxon based on their mapped locations. Using cross-species comparisons and the identified insertion positions, a presence-absence matrix was created for approximately 796,000 insertions. Dollo parsimony analysis of more than 85,000 phylogenetically informative insertions recovered strongly supported, monophyletic clades that correspond with the biogeography of each taxa. This phylogeny is similar to previously published mitochondrial phylogenies, with the exception of the placement of M. vivesi. These results support the utility of our variation on ME-Scan to identify polymorphic retrotransposon insertions in taxa without a reference genome and for large-scale retrotransposon-based phylogenetics.Item Transposable Elements in Bats Show Differential Accumulation Patterns Determined by Class and Functionality(2022) Paulat, Nicole S. (TTU); McGuire, Erin; Subramanian, Krishnamurthy; Osmanski, Austin B. (TTU); Moreno-Santillán, Diana D. (TTU); Ray, David A. (TTU); Xing, JinchuanBat genomes are characterized by a diverse transposable element (TE) repertoire. In particular, the genomes of members of the family Vespertilionidae contain both active retrotransposons and active DNA transposons. Each TE type is characterized by a distinct pattern of accumulation over the past ~40 million years. Each also exhibits its own target site preferences (sometimes shared with other TEs) that impact where they are likely to insert when mobilizing. Therefore, bats provide a great resource for understanding the diversity of TE insertion patterns. To gain insight into how these diverse TEs impact genome structure, we performed comparative spatial analyses between different TE classes and genomic features, including genic regions and CpG islands. Our results showed a depletion of all TEs in the coding sequence and revealed patterns of species- and element-specific attraction in the transcript. Trends of attraction in the distance tests also suggested significant TE activity in regions adjacent to genes. In particular, the enrichment of small, non-autonomous TE insertions in introns and near coding regions supports the hypothesis that the genomic distribution of TEs is the product of a balance of the TE insertion preference in open chromatin regions and the purifying selection against TEs within genes.