De novo transcriptome analysis of an aerial microalga Trentepohlia jolithus: pathway description and gene discovery for carbon fixation and carotenoid biosynthesis.

Qianqian Li,Jianguo Liu,Litao Zhang,Qian Liu

doi:10.1371/journal.pone.0108488

Qianqian Li, Jianguo Liu + Show 2 more

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https://doi.org/10.1371/journal.pone.0108488

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BackgroundAlgae in the order Trentepohliales have a broad geographic distribution and are generally characterized by the presence of abundant β-carotene. The many monographs published to date have mainly focused on their morphology, taxonomy, phylogeny, distribution and reproduction; molecular studies of this order are still rare. High-throughput RNA sequencing (RNA-Seq) technology provides a powerful and efficient method for transcript analysis and gene discovery in Trentepohlia jolithus.Methods/Principal FindingsIllumina HiSeq 2000 sequencing generated 55,007,830 Illumina PE raw reads, which were assembled into 41,328 assembled unigenes. Based on NR annotation, 53.28% of the unigenes (22,018) could be assigned to gene ontology classes with 54 subcategories and 161,451 functional terms. A total of 26,217 (63.44%) assembled unigenes were mapped to 128 KEGG pathways. Furthermore, a set of 5,798 SSRs in 5,206 unigenes and 131,478 putative SNPs were identified. Moreover, the fact that all of the C4 photosynthesis genes exist in T. jolithus suggests a complex carbon acquisition and fixation system. Similarities and differences between T. jolithus and other algae in carotenoid biosynthesis are also described in depth.Conclusions/SignificanceThis is the first broad transcriptome survey for T. jolithus, increasing the amount of molecular data available for the class Ulvophyceae. As well as providing resources for functional genomics studies, the functional genes and putative pathways identified here will contribute to a better understanding of carbon fixation and fatty acid and carotenoid biosynthesis in T. jolithus.

Highlights

The order Trentepohliales (Chlorophyta: Ulvophyceae) is one of the most widespread groups of organisms, and represents an ideal model taxon to investigate evolutionary patterns [1]
The light intensity we measured during daytime ranged from 30 to 2500 mmol photons m22 s21 depending on the degree of cloud cover
The raw assembly contigs were clustered into a unigene dataset, which resulted in 92,414 unigenes that ranged from 200 bp to 9198 bp with a mean length of 619 bp and an N50 length of 986 bp (Table 1)

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Introduction

The order Trentepohliales (Chlorophyta: Ulvophyceae) is one of the most widespread groups of organisms, and represents an ideal model taxon to investigate evolutionary patterns [1] Species of this order are widely distributed over an extensive range of habitats in areas with humid and rainy climates including tropical and temperate regions [2,3,4]. Numerous studies have been carried out on many aspects of the biology of Trentepohlia Many of these monographs are concerned with morphology, taxonomy, phylogeny, distribution and reproduction [2,7,8,9,10,11,12,13]. High-throughput RNA sequencing (RNA-Seq) technology provides a powerful and efficient method for transcript analysis and gene discovery in Trentepohlia jolithus

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