A high-quality chromosome-scale assembly of the centipedegrass [Eremochloa ophiuroides (Munro) Hack.] genome provides insights into chromosomal structural evolution and prostrate growth habit

Centipedegrass [Eremochloa ophiuroides (Munro) Hack.], a member of the Panicoideae subfamily, is one of the most important warm-season turfgrasses originating from China. This grass has an extremely developed prostrate growth habit and has been widely used in transitional and warm climatic regions. To better understand the genetic basis of important biological characteristics, such as prostrate growth and seed yield, in warm-season turfgrasses, we present a high-quality reference genome for centipedegrass and use PacBio, BioNano, and Hi-C technologies to anchor the 867.43 Mb genome assembly into nine pseudochromosomes, with a scaffold N50 of 86.05 Mb and 36,572 annotated genes. Centipedegrass was most closely related to sorghum and diverged from their common ancestor ~16.8 Mya. We detected a novel chromosome reshuffling event in centipedegrass, namely, the nest chromosome fusion event in which fusion of chromosomes 8 and 10 of sorghum into chromosome 3 of centipedegrass likely occurred after the divergence of centipedegrass from sorghum. The typical prostrate growth trait in centipedegrass may be linked to the expansion of candidate PROSTRATE GROWTH 1 (PROG1) genes on chromosome 2. Two orthologous genes of OsPROG1, EoPROG1, and EoPROG2, were confirmed to increase the stem number and decrease the stem angle in Arabidopsis. Collectively, our assembled reference genome of centipedegrass offers new knowledge and resources to dissect the genome evolution of Panicoideae and accelerate genome-assisted breeding and improvement of plant architecture in turf plants.

Use of Transcriptomic Analyses to Elucidate the Mechanism Governing Nodal Root Development in Eremochloa ophiuroides (Munro) Hack.

Centipedegrass [Eremochloa ophiuroides (Munro) Hack.] is a perennial warm-season grass that originated in China, and its speed of nodal rooting is important for lawn establishment. In our study, centipedegrass nodal rooting ability was limited by node aging. Transcriptome sequencing of nodal roots after 0, 2, 4, and 8 days of water culture was performed to investigate the molecular mechanisms of root development. GO enrichment and KEGG pathway analyses of DEGs indicated that plant hormone signal transduction and transcription factors might play important roles in centipedegrass nodal root growth. Among them, E3 ubiquitin-protein ligases participated in multiple hormone signal transduction pathways and interacted with transcription factors. Furthermore, an E3 ubiquitin protein ligase EoSINAT5 overexpressed in rice resulted in longer roots and more numerous root tips, while knockout of LOC_Os07g46560 (the homologous gene of EoSINAT5 in rice) resulted in shorter roots and fewer root tips. These results indicated that EoSINAT5 and its homologous gene are able to promote nodal root development. This research presents the transcriptomic analyses of centipedegrass nodal roots, and may contribute to elucidating the mechanism governing the development of nodal roots and facilitates the use of molecular breeding in improving rooting ability.

Complete Chloroplast Genome Sequence of a Major Warm-Season Turfgrass Species, Centipedegrass [Eremochloa ophiuroides (Munro) Hack.]: Genome Characterization, Comparative and Phylogenetic Analysis

Background: Chloroplast (cp) genome sequence data could provide valuable information for molecular taxonomy and phylogenetic reconstruction among plant species and individuals. However, as one of the most important warm-season turfgrasses widely used in USA and China, cp genome characteristics and phylogenetic position of centipedegrass (Eremochloa ophiuroides) were poorly understood.Results: In this study, we determined the complete chloroplast genome sequences of E. ophiuroides using high-throughput Illumina sequencing technology. The circle pseudomolecule for E. ophiuroides cp genome is 139,107 bp in length, and has a typical quadripartite structure consisting of a pair of inverted repeat (IR) regions of 22,230 bp each separated by a large single copy (LSC) region of 82,081 bp and a small single copy (SSC) region of 12,566 bp. The nucleotide composition of E. ophiuroides cp genome is asymmetric with an overall A + T content of 61.60%. It encodes a total of 131 gene species, composed of 20 duplicated genes within the IR regions and 111 unique genes including 77 protein-coding genes (PCGs), 30 transfer RNA (tRNA) genes and four ribosome RNA (rRNA) genes. Analysis of the repetitive sequences revealed that E. ophiuroides cp genome contains 51 tandem repeats including 29 forward, 20 palindromic and 2 reverse repeats, and 197 simple sequence repeats (SSRs) which were mainly composed of adenine (A) and thymine (T) bases. Comparison of the E. ophiuroides complete cp genome with the genomes of other seven Gramineae species showed a high degree of collinearity among Gramineae plants. Phylogenetic analysis showed that E. ophiuroides was closely related to E. ciliaris and E. eriopoda, and was placed in a clade with the two Eremochloa species and Mnesithea helferi within the subtribe Rottboelliinae, which clarified evolutionary status of E. ophiuroides in tribe Andropogoneae and also authenticated the current taxonomy of the tribe Andropogoneae.Conclusions: The present study provides the complete structure of the E. ophiuroides cp genome, and preliminarily ascertains the phylogenetic position of E. ophiuroides in tribe Andropogonodae. This will be of value to grass taxa identification, phylogenetic resolution, population structure and biodiversity, novel gene discovery and functional genomic studies for the genus Eremochloa.

Complete Chloroplast Genome Sequence of a Major Warm-Season Turfgrass Species, Centipedegrass [Eremochloa ophiuroides (Munro) Hack.]: Genome Characterization, Comparative and Phylogenetic Analysis

Background: Chloroplast (cp) genome sequence data could provide valuable information for molecular taxonomy and phylogenetic reconstruction among plant species and individuals. However, as one of the most important warm-season turfgrasses widely used in USA and China, cp genome characteristics and phylogenetic position of centipedegrass (Eremochloa ophiuroides) were poorly understood.Results: In this study, we determined the complete chloroplast genome sequences of E. ophiuroides using high-throughput Illumina sequencing technology. The circle pseudomolecule for E. ophiuroides cp genome is 139,107 bp in length, and has a typical quadripartite structure consisting of a pair of inverted repeat (IR) regions of 22,230 bp each separated by a large single copy (LSC) region of 82,081 bp and a small single copy (SSC) region of 12,566 bp. The nucleotide composition of E. ophiuroides cp genome is asymmetric with an overall A + T content of 61.60%. It encodes a total of 131 gene species, composed of 20 duplicated genes within the IR regions and 111 unique genes including 77 protein-coding genes (PCGs), 30 transfer RNA (tRNA) genes and four ribosome RNA (rRNA) genes. Analysis of the repetitive sequences revealed that E. ophiuroides cp genome contains 51 tandem repeats including 29 forward, 20 palindromic and 2 reverse repeats, and 197 simple sequence repeats (SSRs) which were mainly composed of adenine (A) and thymine (T) bases. Comparison of the E. ophiuroides complete cp genome with the genomes of other seven Gramineae species showed a high degree of collinearity among Gramineae plants. Phylogenetic analysis showed that E. ophiuroides was closely related to E. ciliaris and E. eriopoda, and was placed in a clade with the two Eremochloa species and Mnesithea helferi within the subtribe Rottboelliinae, which clarified evolutionary status of E. ophiuroides in tribe Andropogoneae and also authenticated the current taxonomy of the tribe Andropogoneae.Conclusions: The present study provides the complete structure of the E. ophiuroides cp genome, and preliminarily ascertains the phylogenetic position of E. ophiuroides in tribe Andropogonodae. This will be of value to grass taxa identification, phylogenetic resolution, population structure and biodiversity, novel gene discovery and functional genomic studies for the genus Eremochloa.

Eremochloa ophiuroides (centipedegrass).

E. ophiuroides is a perennial grass that has been intentionally introduced into tropical and warm temperate areas to be used as a lawn grass (USDA-ARS, 2016). In the United States it has become a common lawn grass principally in the southeastern states (Brosnan and Deputy, 2008; Duble, 2016). However, in the USA, it also behaves as a weed principally in disturbed sites and along roadsides (Coile, 1993; USDA-NRCS, 2016) and Miller et al. (2010) recently reported that it is invading natural and disturbed areas across the southern states. It is also listed as an invasive grass in Puerto Rico (Rojas-Sandoval and Acevedo-Rodríguez, 2015). E. ophiuroides spreads easily by seeds and by stolons and grows forming dense mats of prostrate, low-growing stems and leaves (Brosnan and Deputy, 2008). Plants also recover quickly after fire (Walsh, 1994).

Evidence of Pollinators Foraging on Centipedegrass Inflorescences

Turfgrasses are commonly used for lawns and as recreational surfaces in the USA. Because grasses are largely wind-pollinated, it was thought that pollinators would not forage on turfgrasses. Centipede grass (Eremochloa ophiuroides (Munro) Hack) is a warm-season turfgrass widely used in the southeastern USA. Centipede grass produces spike-like inflorescences from August to October, and little is known about whether pollinators utilize those inflorescences as pollen resources. Thus, the objective of the current study was to identify the pollinators foraging on centipede grass inflorescences. Pollinator samples were collected by (1) sweeping the insects actively foraging on centipede grass inflorescence for 30 min, (2) deploying pan traps for 24 h and (3) deploying malaise traps for 7 d. In the sweep samples, Lasioglossum spp., Bombus spp., Apis spp., Melissodes spp. and Augochlorella spp. were collected from centipede grass inflorescences. Syrphid flies were also collected in the sweep samples. The pan and malaise traps collected mostly Lasioglossum spp. The results imply that there is a critical need to conserve bee habitats and adopt nondisruptive lawn practices. Additionally, this new knowledge lays the foundation for future research to enhance our understanding of bee and syrphid behavior and the selection of host traits for improving bee foraging.