Comparison of Multiple Displacement Amplification (MDA) and Multiple Annealing and Looping-Based Amplification Cycles (MALBAC) in Single-Cell Sequencing

<div><p>Single-cell sequencing promotes our understanding of the heterogeneity of cellular populations, including the haplotypes and genomic variability among different generation of cells. Whole-genome amplification is crucial to generate sufficient DNA fragments for single-cell sequencing projects. Using sequencing data from single sperms, we quantitatively compare two prevailing amplification methods that extensively applied in single-cell sequencing, multiple displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC). Our results show that MALBAC, as a combination of modified MDA and tweaked PCR, has a higher level of uniformity, specificity and reproducibility.</p></div

Pairwise Kendall's τ coefficient test of reads coverage of different samples on autosomes.

<p>Pairwise Kendall's τ coefficient test of reads coverage of different samples on autosomes.</p

The joint distribution of <i>K</i>-mer frequency in two randomly paired samples.

<p>The joint distribution of <i>K</i>-mer frequency in two randomly paired samples.</p

Histogram shows the accordance of <i>K</i>-mer frequency with theoretical Poisson.

<p>Histogram shows the accordance of <i>K</i>-mer frequency with theoretical Poisson.</p

Evaluation of the SNP quality.

<p>Venn diagram shows the SNPs share among (a) MALBAC samples and (b) MDA samples; (c) Histogram represents the rates of SNP recurrence in dbSNP.</p

Genomic coverage on chromosome 1 (Chr01).

<p>Tilling window size is 1 M. (a) Reads counts in each window; (b) Base coverage depth (upper) and uncovered base rate (lower) in each window. Sperm 23∼28 are MDA samples and Sperm S01∼S03 are MALBAC samples. Refer to supplemental figures for other autosomes.</p

进出液方式对全钒液流电池性能影响模拟研究

The phylogenetic tree of R-genes with typical domains showing the different divergence rates among legumes. The numbers above the lines indicate the divergence rates of different R-genes with (A) NBS-LRR, (B) TIR-NBS, (C) CC-NBS-LRR, and (D) CC-NBS domains. (PDF 480 kb

Additional file 7: Figure S5. of Molecular phylogeny and dynamic evolution of disease resistance genes in the legume family

Chromosomal distributions of R-genes in the legume family. The different colors represent different species, and the Y-axis denotes the number of R-genes on each chromosome. Note that the legumes have different chromosomes and some genome assembly was not anchored to chromosomes. (PDF 591 kb

Additional file 2: Figure S1. of Molecular phylogeny and dynamic evolution of disease resistance genes in the legume family

The orthologous gene families within the legumes with grape as the out-group. (A) Category of gene orthologs in legumes; (B) A Venn diagram showing the number of genes common among wild soybean (G. soja), cultivated soybean (G. max), barrel clover (M. truncatula) and chickpea (C. arietinum). (PDF 428 kb

Additional file 6: Figure S4. of Molecular phylogeny and dynamic evolution of disease resistance genes in the legume family

Boxplot showing the lengths of R proteins identified in legumes. The length of an R protein was expressed in number of amino acid residues (aa). (PDF 141 kb