The first transcriptome sequencing and analysis of the endangered plant species Picea neoveitchii Mast. and potential EST-SSR markers development

Abstract

Picea neoveitchii Mast. is a rare and endangered evergreen coniferous tree species in China. P. neoveitchii grows within a specific ecological and geographical range. Here, we performed transcriptome sequencing of P. neoveitchii using the Illumina high-throughput deep sequencing technology with the following aims: (i) to perform de novo transcriptome assembly, (ii) to perform transcriptome assembly with functional annotation, (iii) to study the candidate genes involved in the biosynthesis of cellulose and lignin, (iv) to identify and analyse the transcription factors, and (v) to develop potential expressed sequence tag-simple sequence repeat (EST-SSR) markers for future population genomic and genome-wide association studies in P. neoveitchii. This is, to the best of our knowledge, the first study to provide a comprehensive transcriptome of P. neoveitchii. The transcriptome data contained 12.97 gigabase pairs (Gbp) for a total of 120,951 different transcripts belonging to 66,022 unigenes. In addition, we classified enzymes involved in the biosynthesis of cellulose and lignin and identified and analysed the transcription factors involved in stress responses, growth and development. Based on the larger than 1 kb unigenes, 1,814 EST-SSR markers were shown. Our results demonstrated that the transcriptome analysis is a valuable technology for non-model species with large genomes and this dataset will be an essential resource for future genetic and genomic research in P. neoveitchii.

EST-SSR markers development and application in an important medicinal plant, Schisandra chinensis (Schisandraceae)

“…More than two times higher frequency of the dinucleotides compared to the trinucleotides conformed to the trend as observed in peanut (Arachis hypogaea) [24], precocious trifoliate orange (Citrus reticulata) [29], Korean pine (Picea neoveitchii) [30] and litchi (Litchi chinensis) [31], despite some evidence suggesting that trinucleotides are the most common SSR type [17,19,22,32,33]. This difference is potentially attributed to the characteristics and quantity of EST-SSR and the EST resources in plants.…”

De Novo Transcriptome Profiling for the Generation and Validation of Microsatellite Markers, Transcription Factors, and Database Development for Andrographis paniculata

“…Molecular markers and transcription factors from the transcriptome-based analysis have been generated for several plant species such as Operculina turpethum [38], Chlorophytum borivilianum [39], Ocimum gratissimum [40], Abelmoschus esculentus [41], Platanus acerifolia [42], and Picea neoveitchii Mast. [43], and transcription factor gene-derived microsatellite (TFGM) markers have also been developed in Medicago truncatula [44], Lilium species [45], and Camellia sinensis [46]. In recent years, there has been rapid progress in the generation of genomic resources based on transcriptome sequencing for several plant species, such as Banana (Musa acuminata) [47], Urdbean (Vigna mungo) [48], Noug (Guizotia abyssinica) [49], Tinospora cordifolia [50], and Chickpea (Cicer arietinum) [51].…”