Dogan Mert, Pouch Milan, Mandáková Terezie, Hloušková Petra, Guo Xinyi, Winter Pieter, Chumová Zuzana, Van Niekerk Adriaan, Mummenhoff Klaus, Al-Shehbaz Ihsan A, Mucina Ladislav, Lysak Martin A
CEITEC, Masaryk University, Brno, Czechia.
NCBR, Faculty of Science, Masaryk University, Brno, Czechia.
Front Plant Sci. 2021 Jan 12;11:607893. doi: 10.3389/fpls.2020.607893. eCollection 2020.
The unigeneric tribe Heliophileae encompassing more than 100 species is morphologically the most diverse Brassicaceae lineage. The tribe is endemic to southern Africa, confined chiefly to the southwestern South Africa, home of two biodiversity hotspots (Cape Floristic Region and Succulent Karoo). The monospecific (), the only crucifer species with persistent cotyledons, is traditionally retrieved as the closest relative of Heliophileae. Our transcriptome analysis revealed a whole-genome duplication (WGD) ∼26.15-29.20 million years ago, presumably preceding the / split. The WGD was then followed by genome-wide diploidization, species radiations, and cladogenesis in . The expanded phylogeny based on nuclear ribosomal DNA internal transcribed spacer (ITS) uncovered four major infrageneric clades (A-D) in and corroborated the sister relationship between and . Herein, we analyzed how the diploidization process impacted the evolution of repetitive sequences through low-coverage whole-genome sequencing of 15 species, representing the four clades, and . Despite the firmly established infrageneric cladogenesis and different ecological life histories (four perennials vs. 11 annual species), repeatome analysis showed overall comparable evolution of genome sizes (288-484 Mb) and repeat content (25.04-38.90%) across species and clades. Among species, long terminal repeat (LTR) retrotransposons were the predominant components of the analyzed genomes (11.51-22.42%), whereas tandem repeats had lower abundances (1.03-12.10%). In , the tandem repeat content (17.92%, 16 diverse tandem repeats) equals the abundance of LTR retrotransposons (16.69%). Among the 108 tandem repeats identified in , only 16 repeats were found to be shared among two or more species; no tandem repeats were shared by and genomes. Six "relic" tandem repeats were shared between any two different clades by a common descent. Four and six clade-specific repeats shared among clade A and C species, respectively, support the monophyly of these two clades. Three repeats shared by all clade A species corroborate the recent diversification of this clade revealed by plastome-based molecular dating. Phylogenetic analysis based on repeat sequence similarities separated the species to three clades [A, C, and (B+D)], mirroring the post-polyploid cladogenesis in inferred from rDNA ITS and plastome sequences.
单属的向日葵族包含100多个物种，在形态上是十字花科中最多样化的谱系。该族是南非特有的，主要局限于南非西南部，这里是两个生物多样性热点地区（开普植物区和肉质卡鲁地区）的所在地。单种属（）是唯一具有持久子叶的十字花科物种，传统上被认为是向日葵族最近的亲缘种。我们的转录组分析显示，在大约2615万至2920万年前发生了一次全基因组复制（WGD），大概在/分裂之前。随后是全基因组二倍体化、物种辐射以及在中的分支形成。基于核糖体DNA内部转录间隔区（ITS）的扩展系统发育揭示了中的四个主要属下分支（A - D），并证实了和之间的姐妹关系。在此，我们通过对代表四个分支和的15个物种进行低覆盖度全基因组测序，分析了二倍体化过程如何影响重复序列的进化。尽管属下分支形成已被牢固确立，且生态生活史不同（4个多年生植物与11个一年生植物物种），但重复序列组分析表明，跨物种和分支的基因组大小（288 - 484 Mb）和重复序列含量（25.04 - 38.90%）总体上具有可比的进化情况。在物种中，长末端重复（LTR）逆转座子是分析基因组的主要组成部分（11.51 - 22.42%），而串联重复序列的丰度较低（1.03 - 12.10%）。在中，串联重复序列含量（17.92%，16种不同的串联重复序列）与LTR逆转座子的丰度（16.69%）相当。在中鉴定出的108个串联重复序列中，只有16个重复序列在两个或更多物种中共享；和基因组没有共享的串联重复序列。六个“遗留”串联重复序列通过共同祖先在任何两个不同的分支之间共享。分别在A分支和C分支物种中共享的四个和六个分支特异性重复序列，支持了这两个分支的单系性。所有A分支物种共享的三个重复序列证实了基于质体基因组分子年代测定揭示的该分支最近的多样化。基于重复序列相似性的系统发育分析将物种分为三个分支[A、C和（B + D）]，反映了从rDNA ITS和质体基因组序列推断出的中多倍体后分支形成情况。
