PMC

Categorization of bald cypress HR sequences. The HR sequence reads were classified using the Sequence Read Classification Pipeline of Chouvarine et al. [] with minor modifications detailed in the Materials and Methods. Note that the majority of reads (72.49%) show no significant to homology to known gene or repeat sequences, nor are they categorized as "Probable Repeats" by the SRCP's ab initio repeat analysis functions.

TdCRT1 hybridization to BAC clones. Close-up of a portion of a bald cypress 4 × 4 macroarray probed with the TdCRT1 overgo. Because each clone is double-spotted on the macroarray, positive signals are indicated by closely adjoined dots of similar hybridization intensity (e.g., colored circles). Presumably clones exhibiting the most intense hybridization (e.g., clone in red circle) contain the highest number of TdCRT1 sequences while clones with intermediate or low numbers of TdCRT1 exhibit moderate and low hybridization, respectively (e.g., clones in green and blue circles).

Characterization of the bald cypress BAC library. (A) Size distribution of BAC inserts in the TDD_Ba library as determined by pulsed-field gel electrophoresis (PFGE) of NotI-digested BAC clones. (B) Image of a PFGE gel showing NotI digested BAC clones. The BAC vector is visible as a 7.5 kb band near the bottom of each sample lane. The New England BioLabs Lambda Ladder is shown in the far right lane. (C) Southern blot of the gel shown in B hybridized with bald cypress genomic DNA. Note that some clones exhibit strong hybridization (blue arrows) while others exhibit relatively weak hybridization (red arrows). Clones with strong hybridization signals ostensibly contain more repetitive DNA than those with weak signals.

Cot curve for bald cypress. (A) A least-squares curve (black line) was fit through the data points (gray circles) using the CotQuest program of Bunge et al. []. The curve consists of highly repetitive (HR), moderately repetitive (MR) and single/low copy (SL) components, characterized by fast, intermediate, and slow reassociation, respectively. Blue, green, and red diamonds mark the Cot1/2 values of the HR, MR, and SL components. The brackets centered at a particular Cot1/2 marker show the "two Cot decade region" in which 80% of the sequences in that component will renature []. The blue shaded region at the top of the curve shows the double-stranded HR DNA (plus foldback sequences) isolated for sequencing. Biological data obtained from curve analysis is shown in Table 1. (B) The predicted individual renaturation profiles of the HR component, MR component, and SL component are shown.