Differential genomic arrangements in Caryophyllales through deep transcriptome sequencing of <i>A</i>. <i>hypochondriacus</i>

Genome duplication event in edible dicots under the orders Rosid and Asterid, common during the oligocene period, is missing for species under the order Caryophyllales. Despite this, grain amaranths not only survived this period but display many desirable traits missing in species under rosids and asterids. For example, grain amaranths display traits like C4 photosynthesis, high-lysine seeds, high-yield, drought resistance, tolerance to infection and resilience to stress. It is, therefore, of interest to look for minor genome rearrangements with potential functional implications that are unique to grain amaranths. Here, by deep sequencing and assembly of 16 transcriptomes (86.8 billion bases) we have interrogated differential genome rearrangement unique to Amaranthus hypochondriacus with potential links to these phenotypes. We have predicted 125,581 non-redundant transcripts including 44,529 protein coding transcripts identified based on homology to known proteins and 13,529 predicted as novel/amaranth specific coding transcripts. Of the protein coding de novo assembled transcripts, we have identified 1810 chimeric transcripts. More than 30% and 19% of the gene pairs within the chimeric transcripts are found within the same loci in the genomes of A. hypochondriacus and Beta vulgaris respectively and are considered real positives. Interestingly, one of the chimeric transcripts comprises two important genes, namely DHDPS1, a key enzyme implicated in the biosynthesis of lysine, and alpha-glucosidase, an enzyme involved in sucrose catabolism, in close proximity to each other separated by a distance of 612 bases in the genome of A. hypochondriacus in a convergent configuration. We have experimentally validated that transcripts of these two genes are also overlapping in the 3’ UTR with their expression negatively correlated from bud to mature seed, suggesting a potential link between the high seed lysine trait and unique genome organization.蔷薇类（Rosid）与菊类（Asterid）可食用双子叶植物中普遍发生于渐新世的基因组复制事件，在石竹目（Caryophyllales）类群中缺失。尽管如此，籽粒苋不仅成功渡过该地质时期，还具备诸多蔷薇类与菊类物种所不具备的优良性状。例如，籽粒苋具备C4光合作用、高赖氨酸种子、高产、耐旱、抗侵染及抗逆性等优良性状。因此，探寻籽粒苋所特有的、具备潜在功能意义的小型基因组重排事件具有重要研究价值。本研究通过对16个转录组（总计86.8亿碱基）进行深度测序与组装，解析了尾穗苋（Amaranthus hypochondriacus）特有的、与上述性状存在潜在关联的差异化基因组重排事件。本研究共预测得到125581条非冗余转录本，其中包括44529条基于与已知蛋白同源性鉴定得到的蛋白编码转录本，以及13529条预测为新型/籽粒苋特异性编码转录本。在从头组装得到的蛋白编码转录本中，共鉴定得到1810条嵌合转录本。嵌合转录本中，分别有超过30%和19%的基因对在尾穗苋（A. hypochondriacus）与甜菜（Beta vulgaris）的基因组中位于同一基因座，被认定为真实阳性结果。有趣的是，其中一条嵌合转录本包含两个关键基因：分别为参与赖氨酸生物合成的关键酶DHDPS1，以及参与蔗糖分解代谢的α-葡萄糖苷酶（alpha-glucosidase），二者在尾穗苋基因组中以相向转录构型紧密相邻，间隔仅612个碱基。本研究通过实验验证发现，这两个基因的转录本在3'非翻译区（3' UTR）存在重叠，且从芽期到成熟种子阶段，二者的表达量呈负相关，这提示籽粒苋种子高赖氨酸性状与其独特的基因组组织结构之间存在潜在关联。