Comprehensive analysis of SSRs and database construction using all complete gene-coding sequences in major horticultural and representative plants

Song, Xiaoming; Yang, Qing; Bai, Yun; Gong, Ke; Wu, Tong; Yu, Tong; Pei, Qiaoying; Duan, Weike; Huang, Zhinan; Wang, Zhiyuan; Liu, Zhuo; Kang, Xi; Zhao, Wei; Ma, Xiao

doi:10.1038/s41438-021-00562-7

Cited by 30 publications

(26 citation statements)

References 80 publications

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“…SSRs have been deemed as promising candidate markers for population genetics and germplasm identification in plants due to their hypervariability, high information content and codominance [ 45 , 46 , 47 ]. With the rapid development of next-generation sequencing technology, whole-genome SSR identification becomes much more effective and comprehensive [ 2 , 48 ]. In this study, whole-genome SSR identification and comparative analysis were carried out in five bamboo species including two herbaceous bamboos and three woody bamboos representing three tribes.…”

Section: Discussionmentioning

confidence: 99%

“…Molecular markers usually refer to specific DNA segments that can reflect certain differences in the genomes of individuals or populations, which can directly reveal the genetic information in the organism through DNA molecules [ 1 ]. It is widely used in cultivar identification, marker-assisted selection, and genetic diversity analysis of germplasm resources [ 2 ]. Based on the method of analyses, molecular markers can be divided into three classes: (1) non-PCR-based techniques but based on hybridization, such as restriction fragment length polymorphism (RFLP); (2) PCR-based techniques, such as random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), and simple sequences repeat (SSR); (3) sequence-based marker techniques that is single nucleotide polymorphism (SNP) [ 1 , 3 ].…”

Section: Introductionmentioning

confidence: 99%

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Comprehensive Analyses of Simple Sequence Repeat (SSR) in Bamboo Genomes and Development of SSR Markers with Peroxidase Genes

Liu

Xiao

et al. 2022

Genes

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Simple sequence repeats (SSRs) are one of the most important molecular markers, which are widespread in plants. Bamboos are important forest resources worldwide. Here, the comprehensive identification and comparative analysis of SSRs were performed in three woody and two herbaceous bamboo species. Altogether 567,175 perfect SSRs and 71,141 compound SSRs were identified from 5737.8 Mb genome sequences of five bamboo species. Di-nucleotide SSRs were the most predominant type, with an average of ~50,152.2 per species. Most SSRs were located in intergenic regions, while those located in genic regions were relatively less. Moreover, the results of annotation distribution indicated that terms with P450, peroxidase and ATP-binding cassette transporter related to lignin biosynthesis might play important roles in woody and herbaceous bamboos under the mediation of SSRs. Furthermore, the peroxidase gene family consisted of a large number of genes containing SSRs was selected for the evolutionary relationship analysis and SSR markers development. Fifteen SSR markers derived from peroxidase family genes of Phyllostachys edulis were identified as polymorphic in 34 accessions belonging to seven genera in Bambusoideae. These results provided a comprehensive insight of SSR markers into bamboo genomes, which would facilitate bamboo research related to comparative genomics, evolution and marker-assisted selection.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Comprehensive Analyses of Simple Sequence Repeat (SSR) in Bamboo Genomes and Development of SSR Markers with Peroxidase Genes

Liu

Xiao

et al. 2022

Genes

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“…Interestingly, the three species with the highest percentage of Hsf family genes were all Brassicaceae species. This phenomenon might also relate to the WGD and WGT events of the Brassicaceae species [ 49 – 51 ]. The number of Hsf gene losses was more than gene duplication in most Lycopodiophyta, Gymnospermae, and Angiospermae species, which indicated that the Hsf family genes were lost after the WGD or WGT events in higher plants.…”

Section: Discussionmentioning

confidence: 99%

Large-scale analyses of heat shock transcription factors and database construction based on whole-genome genes in horticultural and representative plants

Bai

Liu

et al. 2022

Horticulture Research

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Heat shock transcription factor (Hsf) plays a critical role in regulating heat resistance. Here, 2950 Hsf family genes were identified from 111 horticultural and representative plants. More Hsf genes were detected in higher plants than lower plants. Based on all Hsf genes, we constructed a phylogenetic tree, which indicated that Hsf genes of each branch evolved independently after species differentiation. Furthermore, we uncovered the evolutionary trajectories of Hsf genes by motif analysis. There were only 6 motifs (M1 to M6) in lower plants, and then 4 novel motifs (M7-M10) appeared in higher plants. However, the motifs of some Hsf genes were lost in higher plant, indicating that Hsf genes have undergone sequence variation during the evolution. The number of Hsf gene loss was more than duplication after whole-genome duplication in higher plants. The heat response network was constructed using 24 Hsf genes, 2421 downstream, and 222 upstream genes of Arabidopsis. Further enrichment analysis revealed that Hsf genes and other transcription factors interacted with each other to response heat resistance. The global expression maps were illustrated for Hsf genes under various abiotic, biotic stresses, and several developmental stages in Arabidopsis. The syntenic and phylogenetic analyses were conducted using Hsf genes of Arabidopsis and Pan-genome of 18 Brassica rapa accessions. We also performed the expression pattern analysis of Hsf and six Hsp family genes using expression values from different tissues and heat treatments in B. rapa. The interaction network between Hsf and Hsp gene families was constructed in B. rapa, and several core genes were detected in the network. Finally, we constructed a Hsf database (http://hsfdb.bio2db.com) for researchers to retrieve Hsf gene family information. Therefore, our study will provide rich resources for the evolution and functional study of Hsf genes.

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“…The software also identifies VNTRS from a large genome size, locates the SSRs in the gene coding region, and statistically analyzes and plots the graphs [ 20 ]. Simple sequence repeats are short repeat DNA sequences with 1–6 bp in length, which have high polymorphism and can be used as a tool in genetic mapping, population genetics, and phylogenetic analysis [ 21 ].…”

Section: Methodsmentioning

confidence: 99%

Integrated Metabolite and Transcriptome Profiling-Mediated Gene Mining of Sida cordifolia Reveals Medicinally Important Genes

Padmanabhan

Natarajan

Palanisamy

2022

Genes

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Sida cordifolia is a medicinal shrub that is conventionally used in the Indian system of medicine;however, the genes contributing to its medicinal properties have been minimally explored, thus limiting its application. High-throughputsequencing and Liquid Chromatography with tandem mass spectrometry(LC-MS/MS) technologies were applied to unravel the medicinally important bioactive compounds. As a result, transcriptomic sequencing generated more than 12 GB of clean data, and 187,215 transcripts were obtained by de novoassembly. These transcripts were broadly classified into 20 classes, based on the gene ontology classification, and 6551 unigenes were annotated using Kyoto Encyclopedia of Genes and Genomes (KEGG) database with more than 142 unigenes involved in the biosynthesis of secondary metabolites. LC-MS/MS analysis of three tissues of Sida cordifolia revealed that acacetin and procyanidin are some important metabolites identified thatcontribute to its medicinal value. Several key enzymes witha crucial role in phenylpropanoid and flavonoid biosynthetic pathways were identified, especially phenylalanine ammonia lyase, which might be an important rate-limiting enzyme. Real-Time Quantitative Reverse Transcription Polymerase chain reaction (qRT-PCR) analysis revealed enzymes, such as Phenylalanine ammonia lyase (PAL), Cinnamyl alcohol dehydrogenase 1 (CAD), Cinnamoyl-CoA reductase 1 (CF1) and Trans cinnamate 4-monooxygenase(TCM), which were predominantly expressed in root compared to leaf and stem tissue. The study provides a speculative insight for the screening of active metabolites and metabolic engineering in Sida cordifolia.

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Comprehensive analysis of SSRs and database construction using all complete gene-coding sequences in major horticultural and representative plants

Cited by 30 publications

References 80 publications

Comprehensive Analyses of Simple Sequence Repeat (SSR) in Bamboo Genomes and Development of SSR Markers with Peroxidase Genes

Comprehensive Analyses of Simple Sequence Repeat (SSR) in Bamboo Genomes and Development of SSR Markers with Peroxidase Genes

Large-scale analyses of heat shock transcription factors and database construction based on whole-genome genes in horticultural and representative plants

Integrated Metabolite and Transcriptome Profiling-Mediated Gene Mining of Sida cordifolia Reveals Medicinally Important Genes

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