Enriching Genomic Resources and Transcriptional Profile Analysis of Miscanthus sinensis under Drought Stress Based on RNA Sequencing

Abstract

Miscanthus × giganteus is wildly cultivated as a potential biofuel feedstock around the world; however, the narrow genetic basis and sterile characteristics have become a limitation for its utilization. As a progenitor of M. × giganteus, M. sinensis is widely distributed around East Asia providing well abiotic stress tolerance. To enrich the M. sinensis genomic databases and resources, we sequenced and annotated the transcriptome of M. sinensis by using an Illumina HiSeq 2000 platform. Approximately 316 million high-quality trimmed reads were generated from 349 million raw reads, and a total of 114,747 unigenes were obtained after de novo assembly. Furthermore, 95,897 (83.57%) unigenes were annotated to at least one database including NR, Swiss-Prot, KEGG, COG, GO, and NT, supporting that the sequences obtained were annotated properly. Differentially expressed gene analysis indicates that drought stress 15 days could be a critical period for M. sinensis response to drought stress. The high-throughput transcriptome sequencing of M. sinensis under drought stress has greatly enriched the current genomic available resources. The comparison of DEGs under different periods of drought stress identified a wealth of candidate genes involved in drought tolerance regulatory networks, which will facilitate further genetic improvement and molecular studies of the M. sinensis.

Unveiling the transcriptomic complexity of Miscanthus sinensis using a combination of PacBio long read- and Illumina short read sequencing platforms

“…Of all the hits to the NR proteins from BLASTX, most transcripts (149,618, ∼49%) were annotated to Sorghum bicolor, followed by Zea mays (59,871; 19.8%) ( Fig. 3b), which is consistent with several previous Miscanthus transcriptome analyses when the sugarcane genome sequences were not yet available [10][11][12]. Thus, it is no surprise that most of our Miscanthus sequences could be mapped to the sugarcane genome but could not be annotated owing to the limited sugarcane genome annotation information in public databases.…”

“…Functional genomic resources of Miscanthus are required to understand the molecular processes underlying their suitability for bioenergetics applications. With the development of new sequencing techniques, transcriptome analysis has been proven to be a very powerful means of gene discovery, genome annotation, and deep exploration of genes that contribute to phenotypic traits [6][7][8][9][10]. A few NGS RNA-Seq transcriptome databases of M. sinensis, M. sacchari orus, and M. lutarioriparius have been reported previously [10,11,42], but these studies were limited by either transcript length and/or the number of transcript isoforms.…”

“…Although several Miscanthus species have been considered important feedstocks for biofuels and biore neries, their genetic resources, including transcriptome data, are currently very limited. Previously, transcriptome pro ling has only been reported for three important Miscanthus species, including M. sinensis, M. sacchari orus, and M. × giganteus, to study their transcriptomic similarity with other grasses, construct genetic maps using NGS based markers, and identify genes probably related to traits like rhizome development and self-incompatibility traits [10][11][12]. Miscanthus sinensis is a genetic diploid (2n = 38) with a genome size of 1C = 2.4-2.6 Gb [13].…”

Unveiling the transcriptomic complexity of Miscanthus sinensis using a combination of PacBio long read- and Illumina short read sequencing platforms

“…The whole genome sequence of Miscanthus is not yet available, but access to functional genomic resources of this species are required to understand the molecular processes underlying their suitability for bioenergetics applications. With the development of new sequencing techniques, transcriptome analysis has been proven to be a very powerful means of gene discovery, genome annotation, and deep exploration of genes that contribute to phenotypic traits [9][10][11]. A few NGS RNA-Seq transcriptome databases of M. sinensis, M. sacchari orus, and M. lutarioriparius have been reported previously [12,13,38], but these studies were limited by either transcript length and/or the number of transcript isoforms.…”

“…For example, extensive transcriptome analyses have been conducted on switchgrass (Panicum virgatum L.), which is another important bioenergy crop widely used for lignocellulosic researches. Comparative transcriptome analyses of different switchgrass ecotypes identi ed many molecular biomarkers of phenotypic traits, which accelerated the development of highyielding switchgrass cultivars [10,11]. Although several Miscanthus species have been considered important feedstocks for biofuels and biore neries, their genetic resources, including transcriptome data, are currently very limited.…”