Laboratory of Genetics, Wageningen University Wageningen, Netherlands.
Laboratory of Genetics, Wageningen University Wageningen, Netherlands ; Laboratory of Bioinformatics, Wageningen University Wageningen, Netherlands.
Front Plant Sci. 2014 Jun 20;5:261. doi: 10.3389/fpls.2014.00261. eCollection 2014.
Noccaea caerulescens is an extremophile plant species belonging to the Brassicaceae family. It has adapted to grow on soils containing high, normally toxic, concentrations of metals such as nickel, zinc, and cadmium. Next to being extremely tolerant to these metals, it is one of the few species known to hyperaccumulate these metals to extremely high concentrations in their aboveground biomass. In order to provide additional molecular resources for this model metal hyperaccumulator species to study and understand the mechanism of adaptation to heavy metal exposure, we aimed to provide a comprehensive database of transcript sequences for N. caerulescens. In this study, 23,830 transcript sequences (isotigs) with an average length of 1025 bp were determined for roots, shoots and inflorescences of N. caerulescens accession "Ganges" by Roche GS-FLEX 454 pyrosequencing. These isotigs were grouped into 20,378 isogroups, representing potential genes. This is a large expansion of the existing N. caerulescens transcriptome set consisting of 3705 unigenes. When translated and compared to a Brassicaceae proteome set, 22,232 (93.2%) of the N. caerulescens isotigs (corresponding to 19,191 isogroups) had a significant match and could be annotated accordingly. Of the remaining sequences, 98 isotigs resembled non-plant sequences and 1386 had no significant similarity to any sequence in the GenBank database. Among the annotated set there were many isotigs with similarity to metal homeostasis genes or genes for glucosinolate biosynthesis. Only for transcripts similar to Metallothionein3 (MT3), clear evidence for an additional copy was found. This comprehensive set of transcripts is expected to further contribute to the discovery of mechanisms used by N. caerulescens to adapt to heavy metal exposure.
蓝藻芥是十字花科的一种极端耐受植物，它已适应在含有高浓度、通常有毒的金属（如镍、锌和镉）的土壤中生长。除了对这些金属具有极强的耐受性外，它还是少数几种已知能够将这些金属高度积累到地上生物量中的物种之一。为了为这个模式金属超积累物种提供更多的分子资源，以研究和理解其适应重金属暴露的机制，我们旨在为 N. caerulescens 提供一个全面的转录序列数据库。在这项研究中，通过 Roche GS-FLEX 454 焦磷酸测序，确定了 N. caerulescens 品系“恒河”的根、茎和花序的 23830 条转录序列（转录本），平均长度为 1025bp。这些转录本被分为 20378 个同基因群，代表潜在的基因。这是对现有的 N. caerulescens 转录组集（由 3705 个单基因组成）的一个大规模扩展。当被翻译成与十字花科蛋白质组集进行比较时，22232 个（93.2%）N. caerulescens 转录本（对应于 19191 个同基因群）有显著匹配，并可以相应注释。其余序列中，98 个转录本类似于非植物序列，1386 个转录本与 GenBank 数据库中的任何序列均无显著相似性。在注释的集合中，有许多转录本与金属稳态基因或硫代葡萄糖苷生物合成基因相似。只有与 Metallothionein3（MT3）相似的转录本，才发现有额外拷贝的明确证据。这组全面的转录本预计将进一步有助于发现 N. caerulescens 适应重金属暴露的机制。
