High-quality RNA isolation from pigment-rich Dendrobium flowers

Khairul-Anuar, Muhammad-Asyraf; Mazumdar, Purabi; Lau, Su-Ee; Tan, Tian Tian; Harikrishna, Jennifer Ann

doi:10.1007/s13205-019-1898-y

Cited by 15 publications

(3 citation statements)

References 31 publications

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“…Total RNA was extracted from the anther samples collected from six Musa cultivars, following the modified CTAB method of Khairul‑Anuar et al . (2019) .…”

Section: Methodsmentioning

confidence: 99%

Pollen viabilities and gene expression profiles across Musa genomes

Mingmanit,

Boonsrangsom,

Sujipuli

et al. 2023

AoB PLANTS

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Banana (Musa spp.) is a major global economic fruit crop. However, cross-pollination from other Musa cultivars grown in nearby plantations results in seeded fruit that exceeds market demand. This study investigated pollen viability and germination and examined the expression profiles of pollen development-related genes across seven Musa genomes (AA, BB, AAA, BBB, AAB, ABB and ABBB). Twenty-three Musa cultivars were assessed for pollen viability using LAO and TTC staining methods. Results revealed that pollen viability obtained from both methods was significantly different among all the studied cultivars. Cultivars carrying BB (diploid) genomes had higher viability percentages than AA (diploid), AAA, BBB, AAB and ABB (triploid) and ABBB (tetraploid) genomes. Germination of the studied cultivars was also investigated on pollen culture medium, with results showing significant differences between the pollen of each cultivar. The best germinating cultivar was TKM (11.0%), carrying BB genome. Expression profiles of pollen development-related genes by RT-qPCR indicated that both TPD1A and MYB80 genes were highly expressed in triploid Musa genomes but the PTC1 gene showed down-regulated expression, resulting in non-viable pollen. Pollen viability, pollen germination and pollen development-related genes differed across Musa cultivars. This knowledge will be useful for the selection of male parents for Musa cross-breeding programs. Pollen viability should also be considered when planning Musa production to avoid seeded fruit.

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“…Total RNA was extracted from the anther samples collected from six Musa cultivars, following the modified CTAB method of Khairul‑Anuar et al . (2019) .…”

Section: Methodsmentioning

confidence: 99%

Pollen viabilities and gene expression profiles across Musa genomes

Mingmanit,

Boonsrangsom,

Sujipuli

et al. 2023

AoB PLANTS

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“…Total RNA was extracted from nineteen leaf samples by phenol-chloroform and lithium-chloride (LiCl) method (Sajeevan et al, 2014; Khairul-Anuar et al, 2019) and then quantified using Nanodrop (Thermo Fisher Scientific, USA) and Agilent 4150 Tapestation system for purity and integrity, respectively. Total RNA purity and integrity analysis was done by bleach agarose gel electrophoresis according to procedure outlined by Aranda et al (2012).…”

Section: Methodsmentioning

confidence: 99%

Virome analyses by next-generation sequencing (NGS) in chilli (Capsicum anuumL.) presented with diverse symptoms phenotype revealed the association of seven plant viruses

Reddy

Hiremath

Muttappagol

et al. 2023

Preprint

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Chilli is an important vegetable and spice crop, is known to be infected by several viruses. Techniques used in diagnosis of plant viral diseases before Next-generation sequencing (NGS) are having limitation of identifying the only known viruses. In the present study, virome analyses in infected chilli leaf samples was carried out using NGS to know the diversity of both known and unknown viruses associated with diseased symptoms. For virome profiling, samples from 19 fields were collected from chilli plants showing leaf curling, vein banding, mosaic, mottling, shoestring/rat tail/filiform/leathery and dull coloured leaves. Viral disease incidence in the surveyed fields varied from 26.66% to 47.50%. Total RNA was extracted from the 19 chilli leaf samples collected from fields and were pooled at equimolar concentration for virome profiling. From the rRNA-depleted pooled total RNA, mRNA and sRNA libraries were prepared and sequenced using Illumina NOVASEQ 6000 platform. Raw sequence data obtained was de novo assembled using three approaches; mRNAome with Trinity, sRNAome with Velvet and whole transcriptome (WT) with SPAdes assembly. Chilli virome, pairwise sequence identity and phylogenetic analyses revealed the presence of seven different viruses; chilli leaf curl virus (ChiLCV) along with its associated alpha and betasatellites, cucumber mosaic virus (CMV), groundnut bud necrosis orthotospovirus (GBNV), pepper cryptic virus-2 (PCV-2), pepper vein yellows virus (PeVYV), bell pepper alphaendornavirus (BPEV) and tobacco vein clearing virus (TVCV). From the virus associated contigs, complete/near-complete genomes for ChiLCV, CMV, PCV-2, PeVYV and BPEV and, partial genomes for GBNV and TVCV were reconstructed from the RNAome. Recombination breakpoint analyses revealed presence of recombination breakpoints in ChiLCV (coat protein and AC4 regions), CMV RNA2 (2a protein region) and P0, P3 and P5 protein regions of PeVYV. viruses identified in the current study are known to be originated from intra and interspecific recombination. Further, all the viruses detected in the pooled RNA sample were validated by PCR and loop mediated isothermal amplification (LAMP) using specific primers designed. Among the seven viruses identified in the study in chilli, PeVYV and BPEV are the first reports from India.

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“…Total RNA was isolated from roots using a modified CTAB method [ 39 ] and treated with DNase I (Invitrogen, Carlsbad, CA, USA) to remove DNA contamination. RNA integrity was verified by electrophoresis on a 1.2% agar gel, and the concentration was quantified using a NanoDrop 1000 (Thermo, Waltham, MA, USA).…”

Section: Methodsmentioning

confidence: 99%

Comparative Transcriptome Analysis of Two Peach Rootstocks Uncovers the Effect of Gene Differential Expression on Nitrogen Use Efficiency

Chen

Liu

Guo

et al. 2022

IJMS

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Nitrogen is an important nutrient element that limits plant growth and yield formation, but excessive nitrogen has negative effects on plants and the environment. It is important to reveal the molecular mechanism of high NUE (nitrogen use efficiency) for breeding peach rootstock and variety with high NUE. In this study, two peach rootstocks, Shannong–1 (S) and Maotao (M), with different NUE were used as materials and treated with 0.1 mM KNO3 for transcriptome sequencing together with the control group. From the results of comparison between groups, we found that the two rootstocks had different responses to KNO3, and 2151 (KCL_S vs. KCL_M), 327 (KNO3_S vs. KCL_S), 2200 (KNO3_S vs. KNO3_M) and 146 (KNO3_M vs. KCL_M) differentially expressed genes (DEGs) were identified, respectively, which included multiple transcription factor families. These DEGs were enriched in many biological processes and signal transduction pathways, including nitrogen metabolism and plant hormone signal transduction. The function of PpNRT2.1, which showed up-regulated expression under KNO3 treatment, was verified by heterologous expression in Arabidopsis. The plant height, SPAD (soil and plant analyzer development) of leaf and primary root length of the transgenic plants were increased compared with those of WT, indicating the roles of PpNRT2.1 in nitrogen metabolism. The study uncovered for the first time the different molecular regulatory pathways involved in nitrogen metabolism between two peach rootstocks and provided gene reserve for studying the molecular mechanism of nitrogen metabolism and theoretical basis for screening peach rootstock or variety with high NUE.

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High-quality RNA isolation from pigment-rich Dendrobium flowers

Cited by 15 publications

References 31 publications

Pollen viabilities and gene expression profiles across Musa genomes

Pollen viabilities and gene expression profiles across Musa genomes

Virome analyses by next-generation sequencing (NGS) in chilli (Capsicum anuumL.) presented with diverse symptoms phenotype revealed the association of seven plant viruses

Comparative Transcriptome Analysis of Two Peach Rootstocks Uncovers the Effect of Gene Differential Expression on Nitrogen Use Efficiency

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