The genome of Cleistogenes songorica provides a blueprint for functional dissection of dimorphic flower differentiation and drought adaptability

Abstract

Summary Cleistogenes songorica (2n = 4x = 40) is a desert grass with a unique dimorphic flowering mechanism and an ability to survive extreme drought. Little is known about the genetics underlying drought tolerance and its reproductive adaptability. Here, we sequenced and assembled a high‐quality chromosome‐level C. songorica genome (contig N50 = 21.28 Mb). Complete assemblies of all telomeres, and of ten chromosomes were derived. C. songorica underwent a recent tetraploidization (~19 million years ago) and four major chromosomal rearrangements. Expanded genes were significantly enriched in fatty acid elongation, phenylpropanoid biosynthesis, starch and sucrose metabolism, and circadian rhythm pathways. By comparative transcriptomic analysis we found that conserved drought tolerance related genes were expanded. Transcription of CsMYB genes was associated with differential development of chasmogamous and cleistogamous flowers, as well as drought tolerance. Furthermore, we found that regulation modules encompassing miRNA, transcription factors and target genes are involved in dimorphic flower development, validated by overexpression of CsAP2_9 and its targeted miR172 in rice. Our findings enable further understanding of the mechanisms of drought tolerance and flowering in C. songorica, and provide new insights into the adaptability of native grass species in evolution, along with potential resources for trait improvement in agronomically important species.

Genome-Wide Analysis and Expression Profiles of the Dof Family in Cleistogenes songorica under Temperature, Salt and ABA Treatment

“…In this study, a total of 50 Dof genes were identified in the C. songorica genome database [ 41 ]. For convenience, these C. songorica Dof genes were named CsDof01 - CsDof50 ( Table S1 ).…”

“…The TBtools software was used to draft the CsDof chromosomal location map to show the distribution of each CsDof gene on the C. songorica chromosome ( Figure 2 ). Referring to the previous study [ 41 ], the 20 chromosome of heterotetraploid C. songorica genome were divided into 2 subgenomes ( Table S1 ). The results showed that 46 of the 50 CsDof genes were located on the 20 chromosomes; however, 4 members ( CsDof45 , CsDof46 , CsDof47 , and CsDof50 ), which were anchored on the scaffolds, could not be located on any C. songorica chromosomes.…”

“…Nevertheless, the specific functions of most Dof genes in C. songorica are still unknown. In recent years, the complete C. songorica genome sequence was obtained by our research group [ 41 ], which provided a foundation to elucidate the Dof gene family structure and expression information in C. songorica under temperature, salt, and ABA treatment. In this study, we analyzed the gene structure, chromosomal location, conserved motifs, phylogenetic relationships, expression profile, and response to abiotic stress of Dof genes in C. songorica .…”

Integrated analysis of co-expression, conserved genes and gene families reveal core regulatory network of heat stress response in Cleistogenes songorica, a xerophyte perennial desert plant

“…Low-quality reads, poly-N sequences from the raw data and reads containing adapters were removed to generate clean reads. Furthermore, HISAT2 software was used to map the clean reads to the C. songorica genome [4,54], and StringTie (1.3.1) was used to quantify the gene expression levels according to the fragments per kilobase of transcript per million fragments (FPKM) method [55]. DEGs were analysed by the DESeq R package.…”

“…Therefore, it is important to determine the genomic, transcriptomic and physiological mechanisms of heat tolerance in plants, which are of great importance to accelerate crops and forages breeding aiming at thermotolerance improvement. Cleistogenes songorica, a C4 plant, is a desert grass that distributed widely in the wild lands in the northwest part of China [4]. C. songorica can grow in semi-arid, arid and desert regions where the annual rainfall ranges from 100 to150 mm.…”