Genome-wide identification and comprehensive analysis reveal potential roles of long non-coding RNAs in fruit development of southern highbush blueberry (Vaccinium corymbosum L.)
IntroductionBlueberries have a high antioxidant content and are produced as healthy food worldwide. Long non-coding RNAs (lncRNAs) are a type of regulatory RNAs that play a variety of roles in plants. Nonetheless, information on lncRNAs and their functions during blueberry fruit development is scarc...
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Frontiers Media S.A.
2022-12-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.1078085/full |
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| author | Shuigen Li Shuigen Li Jiaying Zhang Jiaying Zhang Liqing Zhang Liqing Zhang Xianping Fang Xianping Fang Jun Luo Jun Luo Haishan An Haishan An Xueying Zhang Xueying Zhang |
| author_facet | Shuigen Li Shuigen Li Jiaying Zhang Jiaying Zhang Liqing Zhang Liqing Zhang Xianping Fang Xianping Fang Jun Luo Jun Luo Haishan An Haishan An Xueying Zhang Xueying Zhang |
| author_sort | Shuigen Li |
| collection | DOAJ |
| description | IntroductionBlueberries have a high antioxidant content and are produced as healthy food worldwide. Long non-coding RNAs (lncRNAs) are a type of regulatory RNAs that play a variety of roles in plants. Nonetheless, information on lncRNAs and their functions during blueberry fruit development is scarce in public databases.MethodsIn the present study, we performed genome-wide identification of lncRNAs in a southern highbush blueberry using strand-specific RNA sequencing (ssRNA-Seq). Differentially expressed lncRNAs (DE-lncRNAs) and their potential target genes were analyzed at four stages of fruit development. Cis-regulatory DE-lncRNAs were predicted using co-localization analysis.ResultsThese findings included a total of 25,036 lncRNAs from 17,801 loci. Blueberry lncRNAs had shorter transcript lengths, smaller open reading frame (ORF) sizes, fewer exons, and fewer isoforms than protein-coding RNAs, as well as lower expression levels and higher stage-specificity during fruit development. A total of 105 DE-lncRNAs were identified among the comparison group of PAD vs. CUP, 443 DE-lncRNAs were detected when comparing CUP with PINK fruits, and 285 DE-lncRNAs were revealed when comparing PINK and BLUE fruits. According to Kyoto Encyclopedia of Genes and Genomes annotation, target genes of DE-lncRNAs were primarily enriched in the “Autophagy-other”, “DNA replication”, “Endocytosis”, ‘photosynthesis’ and ‘chlorophyll metabolism’ pathways, suggesting that lncRNAs may pay potential roles in fruit expansion and ripening. Moreover, several lncRNAs have been proposed as cis-regulators of the key genes involved in flavonoid biosynthesis. MSTRG.107242.6, and its putative target gene, BTB/POZ and TAZ domain-containing protein, might play critical roles in anthocyanin accumulation in blueberries.DiscussionThese findings highlight the regulatory function of lncRNAs and aid in elucidating the molecular mechanism underlying blueberry fruit growth. |
| first_indexed | 2024-04-11T13:13:39Z |
| format | Article |
| id | doaj.art-7f4d44dafe8c4322a3901b6c5ccae612 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-11T13:13:39Z |
| publishDate | 2022-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-7f4d44dafe8c4322a3901b6c5ccae6122022-12-22T04:22:28ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-12-011310.3389/fpls.2022.10780851078085Genome-wide identification and comprehensive analysis reveal potential roles of long non-coding RNAs in fruit development of southern highbush blueberry (Vaccinium corymbosum L.)Shuigen Li0Shuigen Li1Jiaying Zhang2Jiaying Zhang3Liqing Zhang4Liqing Zhang5Xianping Fang6Xianping Fang7Jun Luo8Jun Luo9Haishan An10Haishan An11Xueying Zhang12Xueying Zhang13Forest and Fruit Tree Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, ChinaShanghai Key Lab of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai, ChinaForest and Fruit Tree Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, ChinaShanghai Key Lab of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai, ChinaForest and Fruit Tree Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, ChinaShanghai Key Lab of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai, ChinaForest and Fruit Tree Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, ChinaShanghai Key Lab of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai, ChinaForest and Fruit Tree Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, ChinaShanghai Key Lab of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai, ChinaForest and Fruit Tree Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, ChinaShanghai Key Lab of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai, ChinaForest and Fruit Tree Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, ChinaShanghai Key Lab of Protected Horticultural Technology, Shanghai Academy of Agricultural Sciences, Shanghai, ChinaIntroductionBlueberries have a high antioxidant content and are produced as healthy food worldwide. Long non-coding RNAs (lncRNAs) are a type of regulatory RNAs that play a variety of roles in plants. Nonetheless, information on lncRNAs and their functions during blueberry fruit development is scarce in public databases.MethodsIn the present study, we performed genome-wide identification of lncRNAs in a southern highbush blueberry using strand-specific RNA sequencing (ssRNA-Seq). Differentially expressed lncRNAs (DE-lncRNAs) and their potential target genes were analyzed at four stages of fruit development. Cis-regulatory DE-lncRNAs were predicted using co-localization analysis.ResultsThese findings included a total of 25,036 lncRNAs from 17,801 loci. Blueberry lncRNAs had shorter transcript lengths, smaller open reading frame (ORF) sizes, fewer exons, and fewer isoforms than protein-coding RNAs, as well as lower expression levels and higher stage-specificity during fruit development. A total of 105 DE-lncRNAs were identified among the comparison group of PAD vs. CUP, 443 DE-lncRNAs were detected when comparing CUP with PINK fruits, and 285 DE-lncRNAs were revealed when comparing PINK and BLUE fruits. According to Kyoto Encyclopedia of Genes and Genomes annotation, target genes of DE-lncRNAs were primarily enriched in the “Autophagy-other”, “DNA replication”, “Endocytosis”, ‘photosynthesis’ and ‘chlorophyll metabolism’ pathways, suggesting that lncRNAs may pay potential roles in fruit expansion and ripening. Moreover, several lncRNAs have been proposed as cis-regulators of the key genes involved in flavonoid biosynthesis. MSTRG.107242.6, and its putative target gene, BTB/POZ and TAZ domain-containing protein, might play critical roles in anthocyanin accumulation in blueberries.DiscussionThese findings highlight the regulatory function of lncRNAs and aid in elucidating the molecular mechanism underlying blueberry fruit growth.https://www.frontiersin.org/articles/10.3389/fpls.2022.1078085/fullblueberryfruit developmentlncRNARNA-seqanthocyanin biosynthesisflavonoid biosynthesis |
| spellingShingle | Shuigen Li Shuigen Li Jiaying Zhang Jiaying Zhang Liqing Zhang Liqing Zhang Xianping Fang Xianping Fang Jun Luo Jun Luo Haishan An Haishan An Xueying Zhang Xueying Zhang Genome-wide identification and comprehensive analysis reveal potential roles of long non-coding RNAs in fruit development of southern highbush blueberry (Vaccinium corymbosum L.) Frontiers in Plant Science blueberry fruit development lncRNA RNA-seq anthocyanin biosynthesis flavonoid biosynthesis |
| title | Genome-wide identification and comprehensive analysis reveal potential roles of long non-coding RNAs in fruit development of southern highbush blueberry (Vaccinium corymbosum L.) |
| title_full | Genome-wide identification and comprehensive analysis reveal potential roles of long non-coding RNAs in fruit development of southern highbush blueberry (Vaccinium corymbosum L.) |
| title_fullStr | Genome-wide identification and comprehensive analysis reveal potential roles of long non-coding RNAs in fruit development of southern highbush blueberry (Vaccinium corymbosum L.) |
| title_full_unstemmed | Genome-wide identification and comprehensive analysis reveal potential roles of long non-coding RNAs in fruit development of southern highbush blueberry (Vaccinium corymbosum L.) |
| title_short | Genome-wide identification and comprehensive analysis reveal potential roles of long non-coding RNAs in fruit development of southern highbush blueberry (Vaccinium corymbosum L.) |
| title_sort | genome wide identification and comprehensive analysis reveal potential roles of long non coding rnas in fruit development of southern highbush blueberry vaccinium corymbosum l |
| topic | blueberry fruit development lncRNA RNA-seq anthocyanin biosynthesis flavonoid biosynthesis |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.1078085/full |
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