A High Resolution Genetic Map Anchoring Scaffolds of the Sequenced Watermelon Genome

As part of our ongoing efforts to sequence and map the watermelon (Citrullus spp.) genome, we have constructed a high density genetic linkage map. The map positioned 234 watermelon genome sequence scaffolds (an average size of 1.41 Mb) that cover about 330 Mb and account for 93.5% of the 353 Mb of the assembled genomic sequences of the elite Chinese watermelon line 97103 (Citrullus lanatus var. lanatus). The genetic map was constructed using an F8 population of 103 recombinant inbred lines (RILs). The RILs are derived from a cross between the line 97103 and the United States Plant Introduction (PI) 296341-FR (C. lanatus var. citroides) that contains resistance to fusarium wilt (races 0, 1, and 2). The genetic map consists of eleven linkage groups that include 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel) and 36 structure variation (SV) markers and spans ∼800 cM with a mean marker interval of 0.8 cM. Using fluorescent in situ hybridization (FISH) with 11 BACs that produced chromosome-specifc signals, we have depicted watermelon chromosomes that correspond to the eleven linkage groups constructed in this study. The high resolution genetic map developed here should be a useful platform for the assembly of the watermelon genome, for the development of sequence-based markers used in breeding programs, and for the identification of genes associated with important agricultural traits

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Assignment of linkage groups to eleven chromosomes.

<p>Arrowheads are locations of 45S (green) and 5S (red) rDNA sites in photographs D, H and L. Red signals are locations of BACs on each chromosome and 5S rDNA on chromosome 8. (A) to (C) Hybridization of BAC clones 10K19, 60M17 and 51B14 on chromosome 1, 2 and 3, respectively. (D) Hybridization of BAC clone 51N03 (red) and 45S rDNA (green) on chromosome 4. (E) to (G) Hybridization of BAC clones 109C21, 10M24 and 51P08 on chromosome 5, 6 and 7, respectively. (H) Hybridization of BAC clone 51F09 (red) and 5S rDNA (red arrowheads) and 45S rDNA (green arrowheads) on chromosome 8. (I) to (K) Hybridization of BAC clones 51A03, 36G07, 50J01 on chromosome 9, 10 and 11, respectively. (L) FISH pattern on the prometaphase chromosomes using both 5S (red) and 45S rDNA (green) probes. Scale bar = 5 µm.</p

Summary of the watermelon genetic map generated from line 97103× PI 296341-FR recombinant inbred lines.

<p>Summary of the watermelon genetic map generated from line 97103× PI 296341-FR recombinant inbred lines.</p

A high resolution linkage map for anchoring and orienting watermelon genome scaffolds.

<p>Bins and genetic distances in cM are listed on the left, scaffold lengths in Kb are listed on the right. Yellow scaffolds were oriented in forward direction, purple in reverse direction, and blue not oriented. Segregation distortion regions skewed toward line 97103 are labeled green and those skewed toward PI 296341-FR are orange.</p

A schematic diagram of the development of watermelon SSR, InDel and SV markers.

<p>A schematic diagram of the development of watermelon SSR, InDel and SV markers.</p

Plots of genetic vs physical distance for each linkage group.

<p>In each plot, physical distance is on the horizontal axis (in Mb), and genetic distance is on the vertical axis (in cM). The recombination suppression regions (nearly flat in shadow) are predicted to be pericentromeric regions.</p

The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions

Watermelon, Citrullus lanatus, is an important cucurbit crop grown throughout the world. Here we report a high-quality draft genome sequence of the east Asia watermelon cultivar 97103 (2n = 2x = 22) containing 23,440 predicted protein-coding genes. Comparative genomics analysis provided an evolutionary scenario for the origin of the 11 watermelon chromosomes derived from a 7-chromosome paleohexaploid eudicot ancestor. Resequencing of 20 watermelon accessions representing three different C. lanatus subspecies produced numerous haplotypes and identified the extent of genetic diversity and population structure of watermelon germplasm. Genomic regions that were preferentially selected during domestication were identified. Many disease-resistance genes were also found to be lost during domestication. In addition, integrative genomic and transcriptomic analyses yielded important insights into aspects of phloem-based vascular signaling in common between watermelon and cucumber and identified genes crucial to valuable fruit-quality traits, including sugar accumulation and citrulline metabolism