Supplementary Material for: Karyotypes and Distribution of Tandem Repeat Sequences in Brassica nigra Determined by Fluorescence in situ Hybridization

Whole-genome shotgun reads were analyzed to determine the repeat sequence composition in the genome of black mustard, <i>Brassica nigra</i> (L.) Koch. The analysis showed that satellite DNA sequences are very abundant in the black mustard genome. The distribution pattern of 7 new tandem repeats (BnSAT13, BnSAT28, BnSAT68, BnSAT76, BnSAT114, BnSAT180, and BnSAT200) on black mustard chromosomes was visualized using fluorescence in situ hybridization (FISH). The FISH signals of BnSAT13 and BnSAT76 provided useful cytogenetic markers; their position and fluorescence intensity allowed for unambiguous identification of all 8 somatic metaphase chromosomes. A karyotype showing the location and fluorescence intensity of these tandem repeat sequences together with the position of rDNAs and centromeric retrotransposons of <i>Brassica</i> (CRB) was constructed. The establishment of the FISH-based karyotype in <i>B. nigra</i> provides valuable information that can be used in detailed analyses of <i>B. nigra</i> accessions and derived allopolyploid <i>Brassica</i> species containing the B genome.

本研究通过分析全基因组鸟枪法测序读段 (whole-genome shotgun reads)，解析了黑芥（Brassica nigra (L.) Koch）基因组的重复序列组成。结果显示，卫星DNA序列 (satellite DNA sequences) 在黑芥基因组中丰度极高。本研究采用荧光原位杂交 (fluorescence in situ hybridization, FISH) 技术，可视化呈现了7种全新串联重复序列（BnSAT13、BnSAT28、BnSAT68、BnSAT76、BnSAT114、BnSAT180及BnSAT200）在黑芥染色体上的分布模式。其中，BnSAT13与BnSAT76的FISH信号可作为有效的细胞遗传学标记 (cytogenetic markers)：凭借其信号位置与荧光强度，可清晰区分黑芥全部8条体细胞中期染色体 (somatic metaphase chromosomes)。本研究还构建了整合上述串联重复序列的位置、荧光强度，以及核糖体DNA (rDNAs) 和芸苔属着丝粒反转录转座子 (centromeric retrotransposons of Brassica, CRB) 位置的核型 (karyotype)。黑芥基于FISH的核型的建立，可为黑芥种质材料以及含B基因组的衍生异源多倍体芸苔属物种的精细分析提供宝贵的参考信息。