A transcriptome assembly and its annotation for Citrus aurantifolia leaves

Mexican lime (Citrus aurantifolia) is an important economic crop in tropical and sub-tropical areas including the Pacific region of Mexico. Nowadays, is seriously affected by Huanglongbing (HLB) disease, associated to Candidatus Liberibacter asiaticus (CLas). Transcriptomic profile approaches represent the first step to understand the molecular mechanisms involved in the pathogenic process. To date, reference genomes of Citrus sinensis and Citrus clementina is being used for transcriptomic studies in citrus since a reference transcriptome for acid limes including Mexican lime is not available. In the present study, a Citrus aurantifolia de novo transcriptome was generated from leaves tissue including four conditions: asymptomatic CLas-infected plants (early stage of HLB disease, 8 weeks post inoculation, wpi), symptomatic CLas-infected plants (late stage of HLB disease, 16 wpi) and mock-inoculated control plants at both time points, 8 and 16 wpi. Pools of equimolar quantities of total RNA from 5 plants for each experimental condition, were used for cDNA synthesis and construction of a total of four libraries. Hight-throughput sequencing was performed in Illumina NexSeq500 platform, and assembled transcriptome was constructed using Oases (v.0.2.01). After filtering and removal of redundant sequences, 41,600 tentative transcripts (TTs) were produced with a mean length of 1,838 bp, of which 86.13% were over 500 bp in length, N50 of 2,415 bp and full transcriptome length of 76.60 MB. A total of 34,123 (82.18%) TTs had a confident orthologue, 26,614 TTs encoded complete proteins, and 16,426 were non-redundant according to their TAIR10 and UniProtKB identifier (ID). Annotation also revealed that 6,994 of TTs had no significant homology to any other plant gene, even though 1,438 TTs were predicted to code for complete. In the present data set, a complete transcript annotation in excel format, and full-assembled transcriptome in fasta format are provided. This data is the first hybrid transcriptome of Citrus aurantifolia from both healthy and CLas-infected leaves tissue. The de novo assembled transcriptome represents a valuable reference tool for differential expression analysis for Mexican lime and other acid limes in both healthy and pathogen-challenge conditions. Additionally, the data could be useful for citrus breeding programs and designing of novel diagnostic tools.墨西哥莱檬（Citrus aurantifolia）是热带与亚热带区域（含墨西哥太平洋沿岸地区）的重要经济作物。目前其严重受到黄龙病（Huanglongbing, HLB）的侵害，该病害与亚洲韧皮部杆菌（Candidatus Liberibacter asiaticus, CLas）密切相关。转录组图谱分析技术是解析该病害致病过程分子机制的首要研究路径。迄今为止，由于尚无包含墨西哥莱檬在内的酸橙类参考转录组，柑橘类转录组研究多以甜橙（Citrus sinensis）与克莱门氏柑橘（Citrus clementina）的参考基因组作为参照。本研究针对墨西哥莱檬构建了全新的从头转录组，材料取自叶片组织，涵盖四种实验条件：接种后8周（wpi）的无症状CLas侵染植株（HLB病害早期阶段）、接种后16周（wpi）的显症CLas侵染植株（HLB病害晚期阶段），以及两个时间点（8、16 wpi）的空白接种对照植株。将各实验条件下5株植株的总RNA按等摩尔浓度混合后，用于cDNA合成与文库构建，最终共获得4个测序文库。采用Illumina NexSeq500平台开展高通量测序，并通过Oases（v.0.2.01）软件完成转录组组装。经序列过滤与冗余序列剔除后，共得到41600条暂定转录本（tentative transcripts, TTs），其平均长度为1838 bp，其中86.13%的序列长度大于500 bp，N50值为2415 bp，完整转录组总长度达76.60 MB。在这些暂定转录本中，34123条（占比82.18%）存在可靠的同源基因，26614条TTs可编码完整蛋白质，另有16426条TTs依据TAIR10与UniProtKB标识符（ID）被认定为非冗余序列。注释分析进一步显示，6994条TTs未与其他任何植物基因呈现显著同源性，即便其中1438条TTs被预测可编码完整蛋白质。本数据集附带两类文件：Excel格式的完整转录注释文件，以及FASTA格式的完整组装转录组文件。该转录组是首个针对健康与CLas侵染的墨西哥莱檬叶片组织构建的混合转录组。该从头组装的转录组可作为墨西哥莱檬及其他酸橙类作物在健康与病原菌胁迫条件下开展差异表达分析的珍贵参考工具。此外，该数据集还可应用于柑橘育种项目以及新型诊断工具的研发。