Boutte Julien, Maillet Loeiz, Chaussepied Thomas, Letort Sébastien, Aury Jean-Marc, Belser Caroline, Boideau Franz, Brunet Anael, Coriton Olivier, Deniot Gwenaëlle, Falentin Cyril, Huteau Virginie, Lodé-Taburel Maryse, Morice Jérôme, Trotoux Gwenn, Chèvre Anne-Marie, Rousseau-Gueutin Mathieu, Ferreira de Carvalho Julie
IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, France.
IRISA/INRIA, Campus de Beaulieu, Rennes, France.
Front Plant Sci. 2020 Nov 12;11:577536. doi: 10.3389/fpls.2020.577536. eCollection 2020.
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 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 'Z1' genome vs. the '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 'Z1' and 'Chiifu' at the origin of important length differences in some chromosomes. For instance, lengths of 'Z1' and 'Chiifu' A06 chromosomes were estimated to be 55 and 29 Mb, respectively. To validate these observations, we compared using fluorescent 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 accessions corresponding to a 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 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依赖于单个种质的组装，从而掩盖了大多数种内多样性。然而，重排、基因复制和转座元件含量可能对基因组结构产生重大影响，这可能产生新的表型性状。通过比较最近使用长读长技术和光学图谱测序和组装的两个基因组，我们研究了两个种质之间的结构变异和重复序列含量，以及核心种质群体中基因组大小的变异。我们使用比较基因组学和细胞遗传学方法，探讨了“Z1”基因组与“Chifu”基因组中大型重复序列的存在所产生的结构后果。首先，我们发现，在比较“Z1”和“Chifu”时，A05、A06、A09和A10号染色体上的大型基因组变异是由大型插入和倒位引起的，这导致了某些染色体在长度上存在重要差异。例如，“Z1”和“Chifu”的A06号染色体长度估计分别为55 Mb和29 Mb。为了验证这些观察结果，我们使用荧光杂交（FISH）比较了这两个品种杂交产生的F1杂种中存在的两条A06号染色体。我们证实，与“Chifu”相比，“Z1”的A06号染色体长度差异为17.6%。此外，使用拷贝数变异方法，我们能够量化与“Chifu”相比，“Z1”基因组在包括A06号染色体在内的不同染色体上存在更多的rDNA和吉普赛元件。通过流式细胞术，我们估计了对应于可用核心种质群体的12个种质的全基因组大小，结果显示这些种质之间的基因组大小变异高达16%，并且存在一些共同的倒位。这项研究揭示了属于不同栽培群体的新种质长读长测序的贡献，并强调了重复元件差异插入和大型基因组区域倒位对基因组大小种内变异性的潜在影响。
