Identification and characterization of mRNAs and lncRNAs of a barley shrunken endosperm mutant using RNA-seq

Zou, Yaya; Tang, Huaping; Li, Ting; Sun, Min; Qu, Xiangru; Zhou, Jieguang; Yang, Congcong; Mu, Yang; Jiang, Qiantao; Liu, Yaxi; Chen, Guoyue; Chen, Guangdeng; Zheng, Youliang; Wei, Yuming; Lan, Xiujin; Ma, Jian

doi:10.1007/s10709-020-00087-2

Cited by 6 publications

(2 citation statements)

References 83 publications

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“…After assembly of the transcriptome, 70.9% clean reads were successfully mapped to the Rana transcriptome using the Hisat software [16,17]. Gene annotation was performed via BLAST searches of the expressed transcripts (E-value ≤10 − 5 ) against the Nr (NCBI nonredundant protein sequences), Nt (NCBI nucleotide sequences), and Pfam (protein family) databases [18,19]. The accuracy of the assembled transcriptome sequence was tested by PCR.…”

Section: Rpres Gene Identificationmentioning

confidence: 99%

Identification and characterization of amphibian SLC26A5 using RNA-Seq

Wang

et al. 2021

BMC Genomics

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Background Prestin (SLC26A5) is responsible for acute sensitivity and frequency selectivity in the vertebrate auditory system. Limited knowledge of prestin is from experiments using site-directed mutagenesis or domain-swapping techniques after the amino acid residues were identified by comparing the sequence of prestin to those of its paralogs and orthologs. Frog prestin is the only representative in amphibian lineage and the studies of it were quite rare with only one species identified. Results Here we report a new coding sequence of SLC26A5 for a frog species, Rana catesbeiana (the American bullfrog). In our study, the SLC26A5 gene of Rana has been mapped, sequenced and cloned successively using RNA-Seq. We measured the nonlinear capacitance (NLC) of prestin both in the hair cells of Rana’s inner ear and HEK293T cells transfected with this new coding gene. HEK293T cells expressing Rana prestin showed electrophysiological features similar to that of hair cells from its inner ear. Comparative studies of zebrafish, chick, Rana and an ancient frog species showed that chick and zebrafish prestin lacked NLC. Ancient frog’s prestin was functionally different from Rana. Conclusions We mapped and sequenced the SLC26A5 of the Rana catesbeiana from its inner ear cDNA using RNA-Seq. The Rana SLC26A5 cDNA was 2292 bp long, encoding a polypeptide of 763 amino acid residues, with 40% identity to mammals. This new coding gene could encode a functionally active protein conferring NLC to both frog HCs and the mammalian cell line. While comparing to its orthologs, the amphibian prestin has been evolutionarily changing its function and becomes more advanced than avian and teleost prestin.

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Section: Rpres Gene Identificationmentioning

confidence: 99%

Identification and characterization of amphibian SLC26A5 using RNA-Seq

Wang

et al. 2021

BMC Genomics

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“…A lncRNA DRIR regulated the response of Arabidopsis to drought and salt stress [21]. However, some biological functions of lncRNAs have been reported in barley [22,23], such as, about 8000 barley lncRNAs and their expression patterns were found by high-throughput sequencing under excessive boron treatment.Unver et al [24] studied the functional annotation of transcripts co-expressed with lncRNAs, and revealing that molecular function of the ion transport, establishment of localization, and the pure response of leaves to stimulation. The functional role based on lncRNA-mRNA interaction suggestde that lncRNA mediated kinase mediated signal transduction regulates serine / threonine protein kinase SMG1, which may be related to the drought tolerance of wild barley genotype XZ5 [25].…”

Section: Introductionmentioning

confidence: 99%