Transcriptome characterization and screening of molecular markers in ecologically important Himalayan species (Rhododendron arboreum)

Abstract

10Rhododendron arboreum, an ecologically prominent species, also lends commercial and medicinal 11 benefits in the form of palatable juices and useful herbal-drugs. The local abundance and survival of the species 12 under highly fluctuating climate make it an ideal model for genetic structure and functional analysis. However, a 13 lack of genomic data has hampered the additional research. In the present study, cDNA libraries from floral and 14 foliar tissues of the species were sequenced to provide a foundation for understanding the functional aspects of 15 the genome and to construct an enriched repository that will promote genomics studies in the genera. Illumina's 33The Himalayas are among the longest altitude-temperature gradients. The ranges are home to roughly 34 two-thirds of the world's Rhododendron species (subgenus Hymenanthes, family Ericaceae) (Singh et al. 2009). 35The high-altitude flora has specific requirements for humidity, temperature, precipitation, and photoperiod 36 (Gugger et al. 2013; Parmesan and Hanley 2015; Komac et al. 2016). Abiotic factors and their interactions with 37 the genotype of an organism primarily affect its growth and distribution pattern. There are unique microclimates 38 and noticeable topographical gradients in the mountainous regions; even a minor variation in the climate could 39 prove vulnerable to the endemic biodiversity (Thuiller et al. 2005). The resultant upward shift in the snowline 40 has already altered the habitat perimeters and phenological characteristics of many species, counting 41Rhododendron genus as well (Xu et al., 2009). A rise in annual temperature not only influences the population 42 structure of a single species but also threatens the ecosystem as a whole, necessitating a timely evaluation of the 43 associated risks (Memmott et al. 2007; Urban 2015). 44Rhododendron arboreum (2n=26) is dispersed from India to China throughout the Himalayas, 45inhabiting the widest temperature range (4.4-19.3°C) (Vetaas 2002). The genus Rhododendron is a source of 46 useful phytochemicals having potential health benefits (Jaiswal et al. 2012). In addition, the species holds 47 ecological, aesthetic, and commercial eminence in India (Singh et al. 2009; Kumar 2012). Due to the economic 48and medicinal values, the plant is being exploited at a faster rate for harvesting flowers, leaves, and wood. 49Furthermore, a decrease in land cover as a result of anthropogenic activities and global climate changes can 50 cause a decline in the diversity. Despite the varying environmental cues, R. arboreum exploited the earlier 51 trends in climatic conditions, which favored its dominance in the landscapes (Ranjitkar et al. 2013). The 52 inherent genetic variability is very well appreciated for the survival of a species in a specific environment. 56One of the frequently employed marker system in genetic diversity and genotype identification studies 57 is the simple sequence repeat (SSR or microsatellite) marker. SSRs are 1-6 base pairs long tandem repeats 58 present b...

Comparative analysis of microsatellite, SNP, and InDel markers in four <i>Rhododendron</i> species based on RNA-seq

“…However, the least SNP types differed largely in the four species, inferring different gene mutation and molecular evolution occurred. In particular, base transitions were the highest SNP types, ranging from 57.692% ( R. mariesii ) to 60.901% ( R. fortunei ), which were in agreement with that of R. arboreum (60.2%) (Choudhary et al 2018). For InDel markers, the “deletion markers” were more than “insertion markers” in all four species, inferring that “deletion mutation” took place more frequently in Rhododendron species.…”

“…Furthermore, these SNPs could be classified into transitions (purine to purine or pyrimidine to pyrimidine) and transversions (purine to pyrimidine or pyrimidine to purine) (Choudhary et al 2018). In related to these four Rhododendron species, two types of transitions were found, including T:A→C:G and C:G→T:A, while the rest four types (T:A→A:T, T:A→G:C, C:G→G:C, and C:G→A:T) were classified into transversions.…”

“…However, only a few SNPs have been reported in Rhododendron species. From floral and foliar transcriptome of R. arboreum , 811 high-quality SNPs in 719 contigs have been found, including 55.2% transitions, 33.8% transversions, and 9.2% indels (Choudhary et al 2018). In this research, the C:G→T:A SNP was the main type in all four species, followed by T:A→C:G and T:A→A:T types, suggesting that these mutation types occurred more frequently in genomes of Rhododendron species.…”

“…The next generation RNA sequencing (RNA-seq) enables the generation of genomic resources easily, therefore offers critical turning point for relevant Rhododendron research. Besides gene discovery and functional genomics studies, abundant molecular markers could also be developed from transcriptome data (Choudhary et al 2018, Fang et al 2017, Xiao et al 2015, 2018, Xing et al 2017).…”

Elucidation of genetic diversity base in Calotropis procera – a potentially emerging new fibre resource

“…A comparable quality of the assembly for SSR discovery was also achieved by Choudhary et al . (2018). This shows that the quality of our assembly was good for the downstream analysis.…”