Table_1_Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity in Brassica rapa.XLSX

Traditionally, reference genomes in crop species rely on the assembly of one accession, thus occulting most of intraspecific diversity. However, rearrangements, gene duplications, and transposable element content may have a large impact on the genomic structure, which could generate new phenotypic traits. Comparing two Brassica rapa genomes recently sequenced and assembled using long-read technology and optical mapping, we investigated structural variants and repetitive content between the two accessions and genome size variation among a core collection. We explored the structural consequences of the presence of large repeated sequences in B. rapa ‘Z1’ genome vs. the B. rapa ‘Chiifu’ genome, using comparative genomics and cytogenetic approaches. First, we showed that large genomic variants on chromosomes A05, A06, A09, and A10 are due to large insertions and inversions when comparing B. rapa ‘Z1’ and B. rapa ‘Chiifu’ at the origin of important length differences in some chromosomes. For instance, lengths of ‘Z1’ and ‘Chiifu’ A06 chromosomes were estimated in silico to be 55 and 29 Mb, respectively. To validate these observations, we compared using fluorescent in situ hybridization (FISH) the two A06 chromosomes present in an F1 hybrid produced by crossing these two varieties. We confirmed a length difference of 17.6% between the A06 chromosomes of ‘Z1’ compared to ‘Chiifu.’ Alternatively, using a copy number variation approach, we were able to quantify the presence of a higher number of rDNA and gypsy elements in ‘Z1’ genome compared to ‘Chiifu’ on different chromosomes including A06. Using flow cytometry, the total genome size of 12 Brassica accessions corresponding to a B. rapa available core collection was estimated and revealed a genome size variation of up to 16% between these accessions as well as some shared inversions. This study revealed the contribution of long-read sequencing of new accessions belonging to different cultigroups of B. rapa and highlighted the potential impact of differential insertion of repeat elements and inversions of large genomic regions in genome size intraspecific variability.

传统上，作物物种的参考基因组均基于单一种质（accession）的组装，因此遮蔽了绝大多数种内多样性。然而，基因组重排、基因复制以及转座因子（transposable element）组成可能对基因组结构产生显著影响，进而催生新的表型性状。本研究针对近期通过长读长测序技术与光学图谱（optical mapping）组装完成的两份白菜型油菜（Brassica rapa）基因组展开比较分析，探究了两份种质间的结构变异与重复序列组成，以及核心种质集合内的基因组大小变异。本研究借助比较基因组学与细胞遗传学方法，分析了白菜型油菜‘Z1’与‘Chiifu’基因组中大型重复序列差异所带来的结构层面影响。首先，本研究证实，对比‘Z1’与‘Chiifu’两份白菜型油菜种质时，A05、A06、A09及A10号染色体上的大型基因组变异源于大片段插入与倒位，这也是部分染色体长度出现显著差异的根源。例如，通过计算机模拟预测，‘Z1’与‘Chiifu’的A06号染色体长度分别为55 Mb与29 Mb。为验证上述观测结果，本研究针对通过杂交两份种质获得的F1杂交种中的两条A06号染色体开展荧光原位杂交（FISH）比较分析。本研究证实，‘Z1’与‘Chiifu’的A06号染色体长度差异达17.6%。此外，本研究借助拷贝数变异分析方法，量化了‘Z1’基因组中相较于‘Chiifu’更多的核糖体DNA（rDNA）与gypsy型转座因子拷贝数，这类差异在包括A06号染色体在内的多条染色体上均有体现。本研究通过流式细胞术对白菜型油菜核心种质集合中的12份种质进行基因组大小估算，结果显示这些种质间的基因组大小变异最高可达16%，同时还发现了部分共有的染色体倒位。本研究揭示了针对不同栽培类群白菜型油菜新种质开展长读长测序的重要价值，并强调了重复序列差异化插入与大片段基因组区域倒位对于种内基因组大小变异的潜在影响。