De novo assembly and characterization of the root transcriptome and development of simple sequence repeat markers in Paphiopedilum concolor

Abstract

ABSTRACT. Paphiopedilum orchids (Orchidaceae) have attracted much attention from botanists and horticulturists because of their peculiar leaves and beautiful flowers. Furthermore, the dry roots of Paphiopedilum plants have well-known medicinal uses. However, it is unknown how sensitive and plastic the root genes are to environmental changes or how these environmental changes regulate the biosynthesis of active ingredients. In this study, we chose Paphiopedilum concolor for root sequencing, as it is widely used as a parent in breeding experiments. A total of 3.77 Gb of sequence data were generated by Illumina paired-end sequencing. De novo assemblies yielded 72,952 contigs, 67,434 scaffolds, 64,304 unigenes with average lengths of 937, 1022, and 1047 bp, respectively. Based on Basic Local Alignment Search Tool with known protein sequences, 40,815 (63.5%) unigenes were annotated with an E-value cutoff of 1.0E-5. Among the unigenes, 24,605 were classified in the Gene Ontology database, 17,361 were assigned to Cluster of Orthologous Groups, and 14,170 were annotated in Kyoto Encyclopedia of Genes and Genomes. Among these annotations, over 1195 unigenes related to secondary metabolic pathways, as well as 609 unigenes involved in plant hormone synthesis and signal transduction, were identified. In addition, 5322 potential simple sequence repeats (SSRs) were identified, and 4989 primer pairs for 3975 sequences containing SSRs were obtained. This study provides valuable insights into the mechanisms of genes that regulate root growth and development and provides a comprehensive resource for genes related to secondary metabolism in roots and for marker-assisted studies in Paphiopedilum.

Microsatellites characteristics analysis and SSR marker development for Paphiopedilum hirsutissimum based on transcriptome sequencing

“…On average, one SSR loci was found for every 5.42 kb in a unigene, which corresponded to an SSR frequency of 13.06%. The SSR frequency was more than 7.58% of Paphiopedilum concolor (Bateman) Pfitzer (Li et al, 2015b) and consistent with the dicotyledonous SSR frequencies of 2.65-16.82% (Kumpatla and Mukhopadhyay, 2005). The largest fraction of repeat motif was mononucleotide (41.87%), followed by dinucleotide (39.13%) and trinucleotide (18.36%), while tetranucleotide, pentanucleotide and hexanucleotide were just very few numbers of <1% altogether.…”

“…1). The most abundant trinucleotide repeat type was CCG/CGG, such as P. concolor (Li et al , 2015b), which commonly found in monocots (Wang et al , 2011). In contrast, there was no CG/CG repeat identified, which infrequent in plant transcriptome.…”

“…This orchid is listed as a vulnerable species (Vulnerable B2ab) in IUCN Red Lists of Threated Species (). Many studies on this orchid have focused on the transcriptome analysis (Li et al , 2015a, b) and propagation (Ng and Saleh, 2010; Zeng et al , 2012, 2013, 2016) or hybridization (Zeng et al , 2010) of some species in this genus. However, little research has been done on the genetic diversity of P. hirsutissimum .…”

Post genomics era for orchid research

“…Recently, root transcriptome from Paphiopedilum concolor was also produced to explore genes involved in orchid root development (Li et al 2015b ). Over 1195 unique genes participating in secondary metabolic pathways, and 609 ESTs involved in plant hormone biosynthesis, and plant signal transduction were revealed.…”

A Combined Morphological and Molecular Evolutionary Analysis of Karst-Environment Adaptation for the Genus Urophysa (Ranunculaceae)

“…Many calcicoles (species adapted to calcareous soil) have evolved in the region, and their habitats and niches have long been regarded as ‘natural laboratories’ for ecological and evolutionary studies to understand natural selection and species evolution because of the high diversity and unique biota ( Clements et al, 2006 ). Unfortunately, previous studies on karst-specific species are scarce ( Kang et al, 2014 ; Ai et al, 2015 ; Li et al, 2015 ; Liu et al, 2019 ; Feng et al, 2020 ), and until now, the mechanisms of karst environmental adaptation have rarely been examined. Yet such information is important for understanding the survival and adaptive strategies of species in the special karst environmental conditions.…”