Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, PR China.
China Resources Sanjiu Medical & Pharmaceutical Co., Ltd, Shenzhen City, 518000, PR China.
BMC Genomics. 2023 Aug 18;24(1):465. doi: 10.1186/s12864-023-09534-8.
Isatis tinctoria Linnaeus and Isatis indigotica Fortune are very inconsistent in their morphological characteristics, but the Flora of China treats them as the same species. In this work, a new technology that differs from conventional barcodes is developed to prove that they are different species and to clarify their classification.
I. indigotica was indistinguishable from I. tinctoria when using ITS2. CPGAVAS2 was used to construct the chloroplast genomes. MAFFT and DnaSP were used to calculate nucleotide polymorphism, the chloroplast genomes of the two have high diversity in the rpl32 ~ trnL-UAG short region. When using this region as a mini barcode, it was found that there are obvious differences in the base numbers of I. tinctoria and different ploidy I. indigotica were found, but diploid and tetraploid I. indigotica had the same number of bases. Moreover, the reconstruction of the maximum likelihood (ML) tree, utilizing the mini-barcode, demonstrated that I. tinctoria and both diploid and tetraploid I. indigotica are located on distinct branches. The genome size of tetraploid I. indigotica was approximately 643.773 MB, the heterozygosity rate was approximately 0.98%, and the repeat sequence content was approximately 90.43%. This species has a highly heterozygous, extremely repetitive genome.
A new method was established to differentiate between I. indigotica and I. tinctoria. Furthermore, this approach provides a reference and basis for the directional breeding of Isatis.
菘蓝和大青在形态特征上非常不一致，但《中国植物志》将它们视为同一物种。在这项工作中，开发了一种不同于常规条形码的新技术来证明它们是不同的物种，并阐明它们的分类。
I. indigotica 与 I. tinctoria 无法通过 ITS2 区分。使用 CPGAVAS2 构建叶绿体基因组。使用 MAFFT 和 DnaSP 计算核苷酸多态性，两个物种的叶绿体基因组在 rpl32~trnL-UAG 短区域具有高度多样性。当使用这个区域作为一个迷你条形码时，发现菘蓝和不同倍性的大青在碱基数量上存在明显差异，但二倍体和四倍体大青具有相同的碱基数量。此外，利用迷你条形码构建最大似然（ML）树表明，菘蓝和二倍体和四倍体大青都位于不同的分支上。四倍体大青的基因组大小约为 643.773 MB，杂合率约为 0.98%，重复序列含量约为 90.43%。该物种具有高度杂合、极度重复的基因组。
建立了一种区分大青和菘蓝的新方法。此外，该方法为菘蓝属的定向育种提供了参考和依据。
