De Novo Transcriptome Assembly of Anoectochilus roxburghii for Morphological Diversity Assessment and Potential Marker Development
文献类型： 外文期刊
作者： Zhang, Wenting 1 ; Chen, Ke 4 ; Mei, Yu 1 ; Wang, Jihua 1 ;
作者机构： 1.Guangdong Acad Agr Sci, Crop Res Inst, Guangzhou 510640, Peoples R China
2.Guangdong Acad Agr Sci, Guangdong Prov Key Lab Crops Genet & Improvement G, Guangzhou 510640, Peoples R China
3.Guangdong Acad Agr Sci, Guangdong Prov Engn & Technol Res Ctr Conservat &, Guangzhou 510640, Peoples R China
4.Guangdong Acad Agr Sci, Rice Res Inst, Guangzhou 510640, Peoples R China
5.Guangdong Acad Agr Sci, Guangdong Rice Engn Lab, Guangzhou 510640, Peoples R China
6.Guangdong Acad Agr Sci, Minist Agr & Rural Affairs, Key Lab Genet & Breeding High Qual Rice Southern C, Guangzhou 510640, Peoples R China
关键词：
期刊名称：PLANTS-BASEL （ 影响因子：4.1； 五年影响因子：4.5 ）
ISSN： 2223-7747
年卷期： 2024 年 13 卷 23 期
页码：
收录情况： SCI
摘要： Anoectochilus roxburghii is a rare and precious medicinal and ornamental plant of Orchidaceae. Abundant morphological characteristics have been observed among cultivated accessions. Our understanding of the genetic basis of morphological diversity is limited due to a lack of sequence data and candidate genes. In this study, a high-quality de novo transcriptome assembly of A.roxburghii was generated. A total of 138,385 unigenes were obtained, and a BUSCO (Benchmarking Universal Single-Copy Orthologs) analysis showed an assembly completeness of 98.8%. Multiple databases were used to obtain a comprehensive annotation, and the unigenes were functionally categorized using the GO (Gene Ontology), KOG (Eukaryotic Orthologous Groups), KEGG (Kyoto Encyclopedia of Genes and Genomes), and Nr databases. After comparing the phenotypic characteristics of five representative cultivars, a set of cultivar-specific, highly expressed unigenes was identified based on a comparative transcriptome analysis. Then, a WGCNA (Weighted Gene Co-expression Network Analysis) was performed to generate gene regulatory modules related to chlorophyll content (red) and sucrose synthase activity (black). In addition, the expression of six and four GO enrichment genes in the red and black modules, respectively, was analyzed using qRT-PCR to determine their putative functional roles in the leaves of the five cultivars. Finally, in silico SSR (Simple Sequence Repeat) mining of the assembled transcriptome identified 44,045 SSRs. Mononucleotide was the most dominant class of SSRs, followed by complex SSRs. In summary, this study reports on the phenomic and genomic resources of A. roxburghii, combining SSR marker development and validation. This report aids in morphological diversity assessments of Anoectochilus roxburghii.
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