Retracted: Hayai-Annotation Plants: an ultra-fast and comprehensive functional gene annotation system in plants

Ghelfi, Andrea; Shirasawa, Kenta; Hirakawa, Hideki; Isobe, Sachiko

doi:10.1093/bioinformatics/btz380

Cited by 21 publications

(25 citation statements)

References 15 publications

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“…Transcript sequences of sweetpotato were also obtained from the Ipomoea Genome Hub and annotated by Hayai-Annotation Plants (v1.0.2) 51 with a nucleotide sequence identity > 40%, query coverage > 40% and e-value < 10 –6 . GO functional classification of DEGs was performed by WEGO (v2.0) 52 .…”

Section: Methodsmentioning

confidence: 99%

Comparative transcriptome analysis implied a ZEP paralog was a key gene involved in carotenoid accumulation in yellow-fleshed sweetpotato

Suematsu

Tanaka

Kurata

et al. 2020

Sci Rep

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The mechanisms of carotenoid accumulation in yellow-fleshed sweetpotato cultivars are unclear. In this study, we compared the transcriptome profiles of a yellow-fleshed cultivar, Beniharuka (BH) and two of its spontaneous white-fleshed mutants (WH2 and WH3) to reveal the genes involved in yellow flesh. As a result of RNA sequencing, a total of 185 differentially expressed genes (DEGs) were commonly detected in WH2 and WH3 compared to BH. Of these genes, 85 DEGs and 100 DEGs were commonly upregulated and downregulated in WH2 and WH3 compared to BH, respectively. g1103.t1, a paralog of zeaxanthin epoxidase (ZEP), was only DEG common to WH2 and WH3 among 38 genes considered to be involved in carotenoid biosynthesis in storage roots. The expression level of g1103.t1 was also considerably lower in five white-fleshed cultivars than in five yellow-fleshed cultivars. Analysis of carotenoid composition in the storage roots showed that the epoxidised carotenoids were drastically reduced in both WH2 and WH3. Therefore, we propose that the ZEP paralog, g1103.t1, may be involved in carotenoid accumulation through the epoxidation of β-carotene and β-cryptoxanthin in sweetpotato.

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Section: Methodsmentioning

confidence: 99%

Comparative transcriptome analysis implied a ZEP paralog was a key gene involved in carotenoid accumulation in yellow-fleshed sweetpotato

Suematsu

Tanaka

Kurata

et al. 2020

Sci Rep

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“…The two training sets and a preset of SNAP v. 2006-07-28 for Arabidopsis as well as peptide sequences of sweet cherry (v1.0.a1), peach (v2.0.a1) and apple (GDDH13 v1.1) registered in the Genome Database for Rosaceae 50 and those of Japanese apricot 32 were analysed using MAKER pipeline v. 2.31.10 51 to predict putative protein-coding genes in the CYE_r3.1 sequences. Genes annotated using Hayai-Annotation Plants v. 1.0 52 (with a sequence identity threshold of 80% and query coverage of 80%) were selected as a high-confidence gene set.…”

Section: Methodsmentioning

confidence: 99%

Phased genome sequence of an interspecific hybrid flowering cherry, ‘Somei-Yoshino’ (Cerasus × yedoensis)

et al. 2019

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We report the phased genome sequence of an interspecific hybrid, the flowering cherry ‘Somei-Yoshino’ (Cerasus × yedoensis). The sequence data were obtained by single-molecule real-time sequencing technology, split into two subsets based on genome information of the two probable ancestors, and assembled to obtain two haplotype phased genome sequences of the interspecific hybrid. The resultant genome assembly consisting of the two haplotype sequences spanned 690.1 Mb with 4,552 contigs and an N50 length of 1.0 Mb. We predicted 95,076 high-confidence genes, including 94.9% of the core eukaryotic genes. Based on a high-density genetic map, we established a pair of eight pseudomolecule sequences, with highly conserved structures between the two haplotype sequences with 2.4 million sequence variants. A whole genome resequencing analysis of flowering cherries suggested that ‘Somei-Yoshino’ might be derived from a cross between C. spachiana and either C. speciosa or its relatives. A time-course transcriptome analysis of floral buds and flowers suggested comprehensive changes in gene expression in floral bud development towards flowering. These genome and transcriptome data are expected to provide insights into the evolution and cultivation of flowering cherry and the molecular mechanism underlying flowering.

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“…One limitation of Stringtie2 is that only genes corresponding to RNAs expressed with high enough coverage are detected. Unlike gene finding, gene functional annotation has already made the switch to high-throughput automated analysis using tools such as Mercator, TRAPID, or Hayai ( Van Bel et al , 2013 ; Ghelfi et al , 2019 ; Schwacke et al , 2019 ) as well as generalists such as Blast2GO ( Götz et al , 2008 ) to allow for the coming wave of ultra-large genome projects encompassing thousands of species ( Lewin et al , 2018 ).…”

Section: From Oxford Nanopore Technologies Reads To Genomes and Usefumentioning

confidence: 99%

Oxford Nanopore sequencing: new opportunities for plant genomics?

Dumschott

Schmidt

Chawla

et al. 2020

Journal of Experimental Botany

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DNA sequencing was dominated by Sanger’s chain termination method until the mid-2000s, when it was progressively supplanted by new sequencing technologies that can generate much larger quantities of data in a shorter time. At the forefront of these developments, long-read sequencing technologies (third-generation sequencing) can produce reads that are several kilobases in length. This greatly improves the accuracy of genome assemblies by spanning the highly repetitive segments that cause difficulty for second-generation short-read technologies. Third-generation sequencing is especially appealing for plant genomes, which can be extremely large with long stretches of highly repetitive DNA. Until recently, the low basecalling accuracy of third-generation technologies meant that accurate genome assembly required expensive, high-coverage sequencing followed by computational analysis to correct for errors. However, today’s long-read technologies are more accurate and less expensive, making them the method of choice for the assembly of complex genomes. Oxford Nanopore Technologies (ONT), a third-generation platform for the sequencing of native DNA strands, is particularly suitable for the generation of high-quality assemblies of highly repetitive plant genomes. Here we discuss the benefits of ONT, especially for the plant science community, and describe the issues that remain to be addressed when using ONT for plant genome sequencing.

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Retracted: Hayai-Annotation Plants: an ultra-fast and comprehensive functional gene annotation system in plants

Cited by 21 publications

References 15 publications

Comparative transcriptome analysis implied a ZEP paralog was a key gene involved in carotenoid accumulation in yellow-fleshed sweetpotato

Comparative transcriptome analysis implied a ZEP paralog was a key gene involved in carotenoid accumulation in yellow-fleshed sweetpotato

Phased genome sequence of an interspecific hybrid flowering cherry, ‘Somei-Yoshino’ (Cerasus × yedoensis)

Oxford Nanopore sequencing: new opportunities for plant genomics?

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