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EST–SSR Marker Development and Full-Length Transcriptome Sequence Analysis of Tiger Lily (Lilium lancifolium Thunb)

The fast advancement and deployment of sequencing technologies after the Human Genome Project have greatly increased our knowledge of the eukaryotic genome sequences. However, due to technological concerns, high-quality genomic data has been confined to a few key organisms. Moreover, our understandi...

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Autores principales: Sun, Mingwei, Zhao, Yilian, Shao, Xiaobin, Ge, Jintao, Tang, Xueyan, Zhu, Pengbo, Wang, Jiangying, Zhao, Tongli
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8816598/
https://www.ncbi.nlm.nih.gov/pubmed/35126662
http://dx.doi.org/10.1155/2022/7641048
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author Sun, Mingwei
Zhao, Yilian
Shao, Xiaobin
Ge, Jintao
Tang, Xueyan
Zhu, Pengbo
Wang, Jiangying
Zhao, Tongli
author_facet Sun, Mingwei
Zhao, Yilian
Shao, Xiaobin
Ge, Jintao
Tang, Xueyan
Zhu, Pengbo
Wang, Jiangying
Zhao, Tongli
author_sort Sun, Mingwei
collection PubMed
description The fast advancement and deployment of sequencing technologies after the Human Genome Project have greatly increased our knowledge of the eukaryotic genome sequences. However, due to technological concerns, high-quality genomic data has been confined to a few key organisms. Moreover, our understanding of which portions of genomes make up genes and which transcript isoforms synthesize these genes is scarce. Therefore, the current study has been designed to explore the reliability of the tiger lily (Lilium lancifolium Thunb) transcriptome. The PacBio-SMRT was used for attaining the complete transcriptomic profile. We obtained a total of 815,624 CCS (Circular Consensus Sequence) reads with an average length of 1295 bp. The tiger lily transcriptome has been sequenced for the first time using third-generation long-read technology. Furthermore, unigenes (38,707), lncRNAs (6852), and TF members (768) were determined based on the transcriptome data, followed by evaluating SSRs (3319). It has also been revealed that 105 out of 128 primer pairs effectively amplified PCR products. Around 15,608 transcripts were allocated to 25 distinct KOG Clusters, and 10,706 unigenes were grouped into 52 functional categories in the annotated transcripts. Until now, no tiger lily lncRNAs have been discovered. Results of this study may serve as an extensive set of reference transcripts and help us learn more about the transcriptomes of tiger lilies and pave the path for further research.
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spelling pubmed-88165982022-02-05 EST–SSR Marker Development and Full-Length Transcriptome Sequence Analysis of Tiger Lily (Lilium lancifolium Thunb) Sun, Mingwei Zhao, Yilian Shao, Xiaobin Ge, Jintao Tang, Xueyan Zhu, Pengbo Wang, Jiangying Zhao, Tongli Appl Bionics Biomech Research Article The fast advancement and deployment of sequencing technologies after the Human Genome Project have greatly increased our knowledge of the eukaryotic genome sequences. However, due to technological concerns, high-quality genomic data has been confined to a few key organisms. Moreover, our understanding of which portions of genomes make up genes and which transcript isoforms synthesize these genes is scarce. Therefore, the current study has been designed to explore the reliability of the tiger lily (Lilium lancifolium Thunb) transcriptome. The PacBio-SMRT was used for attaining the complete transcriptomic profile. We obtained a total of 815,624 CCS (Circular Consensus Sequence) reads with an average length of 1295 bp. The tiger lily transcriptome has been sequenced for the first time using third-generation long-read technology. Furthermore, unigenes (38,707), lncRNAs (6852), and TF members (768) were determined based on the transcriptome data, followed by evaluating SSRs (3319). It has also been revealed that 105 out of 128 primer pairs effectively amplified PCR products. Around 15,608 transcripts were allocated to 25 distinct KOG Clusters, and 10,706 unigenes were grouped into 52 functional categories in the annotated transcripts. Until now, no tiger lily lncRNAs have been discovered. Results of this study may serve as an extensive set of reference transcripts and help us learn more about the transcriptomes of tiger lilies and pave the path for further research. Hindawi 2022-01-28 /pmc/articles/PMC8816598/ /pubmed/35126662 http://dx.doi.org/10.1155/2022/7641048 Text en Copyright © 2022 Mingwei Sun et al. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Sun, Mingwei
Zhao, Yilian
Shao, Xiaobin
Ge, Jintao
Tang, Xueyan
Zhu, Pengbo
Wang, Jiangying
Zhao, Tongli
EST–SSR Marker Development and Full-Length Transcriptome Sequence Analysis of Tiger Lily (Lilium lancifolium Thunb)
title EST–SSR Marker Development and Full-Length Transcriptome Sequence Analysis of Tiger Lily (Lilium lancifolium Thunb)
title_full EST–SSR Marker Development and Full-Length Transcriptome Sequence Analysis of Tiger Lily (Lilium lancifolium Thunb)
title_fullStr EST–SSR Marker Development and Full-Length Transcriptome Sequence Analysis of Tiger Lily (Lilium lancifolium Thunb)
title_full_unstemmed EST–SSR Marker Development and Full-Length Transcriptome Sequence Analysis of Tiger Lily (Lilium lancifolium Thunb)
title_short EST–SSR Marker Development and Full-Length Transcriptome Sequence Analysis of Tiger Lily (Lilium lancifolium Thunb)
title_sort est–ssr marker development and full-length transcriptome sequence analysis of tiger lily (lilium lancifolium thunb)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8816598/
https://www.ncbi.nlm.nih.gov/pubmed/35126662
http://dx.doi.org/10.1155/2022/7641048
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