A transcriptome assembly and its annotation for Citrus aurantifolia leaves

Published: 01-11-2019| Version 1 | DOI: 10.17632/99tbnvjhsh.1
Ángela Paulina Arce,
Rocío Bautista,
Edgar A. Rodríguez-Negrete,
Miguel Ángel Manzanilla-Ramírez,
José Velázquez,
Jesus Mendez-Lozano,
Eduardo Bejarano,
Araceli G. Castillo,
M. Gonzalo Claros,
Norma Leyva-Lopez


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.