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Zafar UB, Shahzaib M, Atif RM, Khan SH, Niaz MZ, Shahzad K, Chughtai N, Awan FS, Azhar MT, Rana IA. De novo transcriptome assembly of Dalbergia sissoo Roxb. (Fabaceae) under Botryodiplodia theobromae-induced dieback disease. Sci Rep 2023; 13:20503. [PMID: 37993468 PMCID: PMC10665356 DOI: 10.1038/s41598-023-45982-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 10/26/2023] [Indexed: 11/24/2023] Open
Abstract
Dalbergia sissoo Roxb. (Shisham) is a timber-producing species of economic, cultural, and medicinal importance in the Indian subcontinent. In the past few decades, Shisham's dieback disease caused by the fungus Botryodiplodia theobromae has become an evolving issue in the subcontinent endangering its survival. To gain insights into this issue, a standard transcriptome assembly was deployed to assess the response of D. sissoo at the transcriptomic level under the stress of B. theobromae infection. For RNA isolation, the control and infected leaf tissue samples were taken from 1-year-old greenhouse-grown D. sissoo plants after 20 days of stem-base spore inoculation. cDNA synthesis was performed from these freshly isolated RNA samples that were then sent for sequencing. About 18.14 Gb (Giga base) of data was generated using the BGISEQ-500 sequencing platform. In terms of Unigenes, 513,821 were identified after a combined assembly of all samples and then filtering the abundance. The total length of Unigenes, their average length, N50, and GC-content were 310,523,693 bp, 604 bp, 1,101 bp, and 39.95% respectively. The Unigenes were annotated using 7 functional databases i.e., 200,355 (NR: 38.99%), 164,973 (NT: 32.11%), 123,733 (Swissprot: 24.08%), 142,580 (KOG: 27.75%), 139,588 (KEGG: 27.17%), 99,752 (GO: 19.41%), and 137,281 (InterPro: 26.72%). Furthermore, the Transdecoder detected 115,762 CDS. In terms of SSR (Simple Sequence Repeat) markers, 62,863 of them were distributed on 51,508 Unigenes and on the predicted 4673 TF (Transcription Factor) coding Unigenes. A total of 16,018 up- and 19,530 down-regulated Differentially Expressed Genes (DEGs) were also identified. Moreover, the Plant Resistance Genes (PRGs) had a count of 9230. We are hopeful that in the future, these identified Unigenes, SSR markers, DEGs and PRGs will provide the prerequisites for managing Shisham dieback disease, its breeding, and in tree improvement programs.
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Affiliation(s)
- Ummul Buneen Zafar
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Muhammad Shahzaib
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Rana Muhammad Atif
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Sultan Habibullah Khan
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
- National Center for Genome Editing (Gene Editing of Biological Agents for Nutritional, Biochemicals and Therapeutic Purposes), University of Agriculture, Faisalabad, Punjab, Pakistan
| | - Muhammad Zeeshan Niaz
- Plant Pathology Research Institute, Ayub Agriculture Research Institute, Faisalabad, 38850, Punjab, Pakistan
| | - Khalid Shahzad
- Punjab Forestry Research Institute, Faisalabad, 37620, Punjab, Pakistan
| | - Nighat Chughtai
- Punjab Forestry Research Institute, Faisalabad, 37620, Punjab, Pakistan
| | - Faisal Saeed Awan
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Muhammad Tehseen Azhar
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Iqrar Ahmad Rana
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan.
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan.
- National Center for Genome Editing (Gene Editing of Biological Agents for Nutritional, Biochemicals and Therapeutic Purposes), University of Agriculture, Faisalabad, Punjab, Pakistan.
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Darshan K, Aggarwal R, Bashyal BM, Singh J, Saharan MS, Gurjar MS, Solanke AU. Characterization and development of transcriptome-derived novel EST-SSR markers to assess genetic diversity in Chaetomium globosum. 3 Biotech 2023; 13:379. [PMID: 37900266 PMCID: PMC10600081 DOI: 10.1007/s13205-023-03794-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/25/2023] [Indexed: 10/31/2023] Open
Abstract
Chaetomium globosum Kunze, an internationally recognized biocontrol fungus. It mycoparasitizes various plant pathogens and produce antifungal metabolites to suppress the growth of pathogenic fungi. Lack of detailed genome level diversity studies has delimited the development and utilization of potential C. globosum strains. The present study was taken to reveal the distribution, identification, and characterization of expressed sequence tag-simple sequence repeats (EST-SSRs) in C. globosum. RNA-Seq experiment was performed for C. globosum potential isolate Cg2 (AY429049) using Illumina HiSeq 2500. Reference-guided de novo assembly yielded 45,582 transcripts containing 27,957 unigenes. We generated a new set of 8485 EST-SSR markers distributed in 5908 unigene sequences with one SSR locus distribution density per 6.1 kb. Six distinct classes of SSR repeat motifs were identified. The most abundant were mononucleotide repeats (51.67%), followed by tri-nucleotides (36.61%). Out of 5034 EST-SSR primers, 50 primer pairs were selected and validated for the polymorphic study of 15 C. globosum isolates. Twenty-two SSR markers showed average genetic polymorphism among C. globosum isolates. The number of alleles (Na) per marker ranges from 2 to 4, with a total of 74 alleles detected for 22 markers with a mean polymorphism information content (PIC) value of 0.4. UPGMA hierarchical clustering analysis generated three main clusters of C. globosum isolates and exhibited a lower similarity index range from 0.59 to 0.85. Thus, the newly developed EST-SSR markers could replace traditional methods for determining diversity. The study will also enhance the genomic research in C. globosum to explore its biocontrol potential against phytopathogens. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03794-7.
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Affiliation(s)
- K. Darshan
- Division of Plant Pathology, Fungal Molecular Biology Laboratory, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
- Forest Protection Division, ICFRE-Tropical Forest Research Institute, Jabalpur, Madhya Pradesh 482021 India
| | - Rashmi Aggarwal
- Division of Plant Pathology, Fungal Molecular Biology Laboratory, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Bishnu Maya Bashyal
- Division of Plant Pathology, Fungal Molecular Biology Laboratory, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Jagmohan Singh
- Division of Plant Pathology, Fungal Molecular Biology Laboratory, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - M. S. Saharan
- Division of Plant Pathology, Fungal Molecular Biology Laboratory, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - M. S. Gurjar
- Division of Plant Pathology, Fungal Molecular Biology Laboratory, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Amolkumar U. Solanke
- ICAR-National Institute for Plant Biotechnology, ICAR-IARI, New Delhi, 110012 India
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Li H, Song K, Li B, Zhang X, Wang D, Dong S, Yang L. CRISPR/Cas9 Editing Sites Identification and Multi-Elements Association Analysis in Camellia sinensis. Int J Mol Sci 2023; 24:15317. [PMID: 37894996 PMCID: PMC10607008 DOI: 10.3390/ijms242015317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/02/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
CRISPR/Cas9 is an efficient genome-editing tool, and the identification of editing sites and potential influences in the Camellia sinensis genome have not been investigated. In this study, bioinformatics methods were used to characterise the Camellia sinensis genome including editing sites, simple sequence repeats (SSRs), G-quadruplexes (GQ), gene density, and their relationships. A total of 248,134,838 potential editing sites were identified in the genome, and five PAM types, AGG, TGG, CGG, GGG, and NGG, were observed, of which 66,665,912 were found to be specific, and they were present in all structural elements of the genes. The characteristic region of high GC content, GQ density, and PAM density in contrast to low gene density and SSR density was identified in the chromosomes in the joint analysis, and it was associated with secondary metabolites and amino acid biosynthesis pathways. CRISPR/Cas9, as a technology to drive crop improvement, with the identified editing sites and effector elements, provides valuable tools for functional studies and molecular breeding in Camellia sinensis.
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Affiliation(s)
| | | | | | | | | | | | - Long Yang
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai’an 271018, China
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Ning HJ, Gui FF, Tian EW, Yang LY. The novel developed microsatellite markers revealed potential hybridization among Cymbidium species and the interspecies sub-division of C. goeringii and C. ensifolium. BMC PLANT BIOLOGY 2023; 23:492. [PMID: 37833649 PMCID: PMC10571305 DOI: 10.1186/s12870-023-04499-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND Orchids (Cymbidium spp.) exhibit significant variations in floral morphology, pollinator relations, and ecological habitats. Due to their exceptional economic and ornamental value, Cymbidium spp. have been commercially cultivated for centuries. SSR markers are extensively used genetic tools for biology identification and population genetics analysis. RESULT In this study, nine polymorphic EST-SSR loci were isolated from Cymbidium goeringii using RNA-Seq technology. All nine SSR loci showed transferability in seven other congeneric species, including 51 cultivars. The novel SSR markers detected inter-species gene flow among the Cymbidium species and intra-species sub-division of C. goeringii and C. ensifolium, as revealed by neighborhood-joining and Structure clustering analyses. CONCLUSION In this study, we developed nine microsatellites using RNA-Seq technology. These SSR markers aided in detecting potential gene flow among Cymbidium species and identified the intra-species sub-division of C. goeringii and C. ensifolium.
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Affiliation(s)
- Hui-Juan Ning
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, School of Landscape and Architecture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Fang-Fang Gui
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, School of Landscape and Architecture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - En-Wei Tian
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 515005, China.
- Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Guangzhou, 510515, China.
| | - Li-Yuan Yang
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, School of Landscape and Architecture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China.
- Key Laboratory of National Forestry and Grassland Administration On Germplasm Innovation and Utilization for Southern Garden Plants, Hangzhou, 311300, Zhejiang, China.
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Savadi S, Muralidhara BM, Venkataravanappa V, Adiga JD. Genome-wide survey and characterization of microsatellites in cashew and design of a web-based microsatellite database: CMDB. FRONTIERS IN PLANT SCIENCE 2023; 14:1242025. [PMID: 37670858 PMCID: PMC10475544 DOI: 10.3389/fpls.2023.1242025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 07/31/2023] [Indexed: 09/07/2023]
Abstract
The cashew is an edible tree nut crop having a wide range of food and industrial applications. Despite great economic importance, the genome-wide characterization of microsatellites [simple sequence repeats (SSRs)] in cashew is lacking. In this study, we carried out the first comprehensive genome-wide microsatellites/SSRs characterization in cashew and developed polymorphic markers and a web-based microsatellite database. A total of 54526 SSRs were discovered in the cashew genome, with a mean frequency of 153 SSRs/Mb. Among the mined genome-wide SSRs (2-6 bp size motifs), the dinucleotide repeat motifs were dominant (68.98%) followed by the trinucleotides (24.56%). The Class I type of SSRs (≥20 bp) were 45.10%, while Class II repeat motifs (≥12-<20 bp) were 54.89% of the total genomic SSRs discovered here. Further, the AT-rich SSRs occurred more frequently in the cashew genome (84%) compared to the GC-rich SSRs. The validation of the in silico-mined genome-wide SSRs by PCR screening in cashew genotypes resulted in the development of 59 polymorphic SSR markers, and the polymorphism information content (PIC) of the polymorphic SSR markers ranged from 0.19 to 0.84. Further, a web-based database, "Cashew Microsatellite Database (CMDB)," was constructed to provide access to the genome-wide SSRs mined in this study as well as transcriptome-based SSRs from our previous study to the research community through a user-friendly searchable interface. Besides, CMDB provides information on experimentally validated SSRs. CMDB permits the retrieval of SSR markers information with the customized search options. Altogether, the genome-wide SSRs characterization, the polymorphic markers and CMDB database developed in this study would serve as valuable marker resources for DNA fingerprinting, germplasm characterization, genetic studies, and molecular breeding in cashew and related Anacardium species.
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Affiliation(s)
- Siddanna Savadi
- ICAR- Directorate of Cashew Research (DCR), Puttur, Karnataka, India
| | - B. M. Muralidhara
- ICAR-Indian Institute of Horticultural Research (IIHR), CHES, Madikeri, Karnataka, India
| | - V. Venkataravanappa
- ICAR-Indian Institute of Horticultural Research (IIHR), CHES, Madikeri, Karnataka, India
| | - J. D. Adiga
- ICAR- Directorate of Cashew Research (DCR), Puttur, Karnataka, India
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Yoon WS, Kim CK, Kim YK. The First Complete Chloroplast Genome of Campanula carpatica: Genome Characterization and Phylogenetic Diversity. Genes (Basel) 2023; 14:1597. [PMID: 37628648 PMCID: PMC10454809 DOI: 10.3390/genes14081597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 07/28/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023] Open
Abstract
Campanula carpatica is an ornamental flowering plant belonging to the family Campanulaceae. The complete chloroplast genome of C. carpatica was obtained using Illumina HiSeq X and Oxford Nanopore (Nanopore GridION) platforms. The chloroplast genome exhibited a typical circular structure with a total length of 169,341 bp, comprising a large single-copy region of 102,323 bp, a small single-copy region of 7744 bp, and a pair of inverted repeats (IRa/IRb) of 29,637 bp each. Out of a total 120 genes, 76 were protein-coding genes, 36 were transfer RNA genes, and eight were ribosomal RNA genes. The genomic characteristics of C. carpatica are similar to those of other Campanula species in terms of repetitive sequences, sequence divergence, and contraction/expansion events in the inverted repeat regions. A phylogenetic analysis of 63 shared genes in 16 plant species revealed that Campanula zangezura is the closest relative of C. carpatica. Phylogenetic analysis indicated that C. carpatica was within the Campanula clade, and C. pallida occupied the outermost position of that clade.
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Affiliation(s)
- Won-Sub Yoon
- Department of Mechanical Design Engineering, Wonkwang University, Iksan 54538, Republic of Korea
| | - Chang-Kug Kim
- Genomics Division, National Institute of Agricultural Sciences, Jeonju 54874, Republic of Korea;
| | - Yong-Kab Kim
- Department of Information Communication Engineering, Wonkwang University, Iksan 54538, Republic of Korea
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Yerzhebayeva R, Didorenko S, Amangeldiyeva A, Daniyarova A, Mazkirat S, Zinchenko A, Shavrukov Y. Marker-Assisted Selection for Early Maturing E Loci in Soybean Yielded Prospective Breeding Lines for High Latitudes of Northern Kazakhstan. Biomolecules 2023; 13:1146. [PMID: 37509181 PMCID: PMC10377072 DOI: 10.3390/biom13071146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/16/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
The photoperiodic sensitivity of soybean (Glycine max L.) is one of the limiting factors affecting plant growth and yield. At higher latitudes, early flowering and maturity with neutral reaction to photoperiods are required for adaptation of soybean plants to long-day conditions. Currently, the production and distribution of new varieties of soybeans adapted to widespread agricultural regions in northern Kazakhstan is in strong demand. Eleven soybean hybrid populations were obtained from crosses between 17 parents with four maturity groups, MG 000, 00, 0, and I. Marker-assisted selection (MAS) was assessed for suitable SSR markers and successfully applied for genes E1, E3, E4, and E7, targeting homozygous genotypes with recessive alleles. The identified and selected genotypes were propagated and tested in the conditions of 53° N latitude in the Kostanay region of northern Kazakhstan. Finally, 20 early maturing F4 breeding lines were identified and developed with genotypes e1 e3 E4 e7, e1 E3 E4 e7, and e1 E3 e4 e7, all completing their growth period within 92-102 days. These breeding lines were developed by MAS and should provide very prospective superior varieties of soybean for northern Kazakhstan through a strategy that may be very helpful to other countries with high latitudes.
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Affiliation(s)
- Raushan Yerzhebayeva
- Kazakh Research Institute of Agriculture and Plant Growing, Almaty District, Almalybak 040909, Kazakhstan
| | - Svetlana Didorenko
- Kazakh Research Institute of Agriculture and Plant Growing, Almaty District, Almalybak 040909, Kazakhstan
| | - Aigul Amangeldiyeva
- Kazakh Research Institute of Agriculture and Plant Growing, Almaty District, Almalybak 040909, Kazakhstan
| | - Aliya Daniyarova
- Kazakh Research Institute of Agriculture and Plant Growing, Almaty District, Almalybak 040909, Kazakhstan
| | - Shynar Mazkirat
- Kazakh Research Institute of Agriculture and Plant Growing, Almaty District, Almalybak 040909, Kazakhstan
| | - Alyona Zinchenko
- Breeding Station 'Zarechnoe', Kostanay District, Zarechnoe 111108, Kazakhstan
| | - Yuri Shavrukov
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA 5042, Australia
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Itoo H, Shah RA, Qurat S, Jeelani A, Khursheed S, Bhat ZA, Mir MA, Rather GH, Zargar SM, Shah MD, Padder BA. Genome-wide characterization and development of SSR markers for genetic diversity analysis in northwestern Himalayas Walnut ( Juglans regia L.). 3 Biotech 2023; 13:136. [PMID: 37124992 PMCID: PMC10130282 DOI: 10.1007/s13205-023-03563-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 04/15/2023] [Indexed: 05/02/2023] Open
Abstract
In the present study, we designed and validated genome-wide polymorphic SSR markers (110 SSRs) by mining the walnut genome. A total of 198,924 SSR loci were identified. Among these, successful primers were designed for 162,594 (81.73%) SSR loci. Dinucleotides were the most predominant accounting for 88.40% (175,075) of total SSRs. The SSR frequency was 377.312 SSR/Mb and it showed a decreasing trend from dinucleotide to octanucleotide motifs. We identified 20 highly polymorphic SSR markers and used them to genotype 72 walnut accessions. Over all, we obtained 118 alleles that ranged from 2 to 12 with an average value of 5.9. The higher SSR PIC values indicate their robustness in discriminating walnut genotypes. Heat map, PCA, and population structure categorized 72 walnut genotypes into 2 distinct clusters. The genetic variation within population was higher than among population as inferred by analysis of molecular variance (AMOVA). For walnut improvement, it is necessary to have a large repository of SSRs with high discriminative power. The present study reports 150,000 SSRs, which is the largest SSR repository for this important nut crop. Scientific communities may use this repository for walnut improvement such as QTL mapping, genetic studies, linkage map construction, and marker-assisted selection. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03563-6.
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Affiliation(s)
- H. Itoo
- Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K 192303 India
| | - Rafiq Ahmad Shah
- Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K 192303 India
| | - S. Qurat
- Division of Fruit Science, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Faculty of Horticulture, Shalimar, Kashmir, Srinagar, J&K 190 025 India
| | - Afnan Jeelani
- Division of Fruit Science, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Faculty of Horticulture, Shalimar, Kashmir, Srinagar, J&K 190 025 India
| | - Sheikh Khursheed
- Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K 192303 India
| | - Zahoor A. Bhat
- Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K 192303 India
| | - M. A. Mir
- Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K 192303 India
| | - G. H. Rather
- Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K 192303 India
| | - Sajad Majeed Zargar
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Faculty of Horticulture, Shalimar, Kashmir, Srinagar, J&K 190 025 India
| | - M. D. Shah
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Kashmir, 190 025 Srinagar, J&K India
| | - Bilal A. Padder
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Kashmir, 190 025 Srinagar, J&K India
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Habibi N, Al Salameen F, Vyas N, Rahman M, Kumar V, Shajan A, Zakir F, Razzack NA, Al Doaij B. Genome survey and genetic characterization of Acacia pachyceras O. Schwartz. FRONTIERS IN PLANT SCIENCE 2023; 14:1062401. [PMID: 36875582 PMCID: PMC9979705 DOI: 10.3389/fpls.2023.1062401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Acacia pachyceras O. Schwartz (Leguminoseae), a woody tree growing in Kuwait is critically endangered. High throughput genomic research is immediately needed to formulate effective conservation strategies for its rehabilitation. We therefore, performed a genome survey analysis of the species. Whole genome sequencing generated ~97 Gb of raw reads (92x coverage) with a per base quality score above Q30. The k-mer analysis (17 mer) revealed its genome to be 720Mb in size with an average guanine-cytosine (GC) ratio of 35%. The assembled genome was analyzed for repeat regions (45.4%-interspersed repeats; 9%-retroelements; 2%-DNA transposons). BUSCO assessment of completeness of genome identified 93% of assembly to be complete. Gene alignments in BRAKER2 yielded 34,374 transcripts corresponding to 33,650 genes. Average length of coding sequences and protein sequences were recorded as 1,027nts and 342aa, respectively. GMATA software filtered a total of 901,755 simple sequence repeats (SSRs) regions against which 11,181 unique primers were designed. A subset of 110 SSR primers were PCR validated and demonstrated for its application in genetic diversity analysis of Acacia. The SSR primers successfully amplified A. gerrardii seedlings DNA depicting cross transferability among species. The principal coordinate analysis and the split decomposition tree (bootstrapping runs of 1000 replicates) distributed the Acacia genotypes into two clusters. The flow cytometry analysis revealed the A. pachyceras genome to be polyploid (6x). The DNA content was predicted as 2.46 pg, 1.23 pg, and 0.41 pg corresponding to 2C DNA, 1C DNA and 1Cx DNA, respectively. The results provide a base for further high throughput genomic studies and molecular breeding for its conservation.
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Affiliation(s)
- Nazima Habibi
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Kuwait, Kuwait
| | - Fadila Al Salameen
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Kuwait, Kuwait
| | - Nishant Vyas
- Department of Immunology, Logical Life Sciences, Pune, India
| | - Muhammad Rahman
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Kuwait, Kuwait
| | - Vinod Kumar
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Kuwait, Kuwait
| | - Anisha Shajan
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Kuwait, Kuwait
| | - Farhana Zakir
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Kuwait, Kuwait
| | - Nasreem Abdul Razzack
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Kuwait, Kuwait
| | - Bashayer Al Doaij
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Kuwait, Kuwait
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Whole Genome Wide SSR Markers Identification Based on ddRADseq Data. Methods Mol Biol 2023; 2638:59-66. [PMID: 36781635 DOI: 10.1007/978-1-0716-3024-2_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
The advent of advanced NGS technologies have led to the generation of enormous amount of sequence data which further aid in the discovery of the various type of markers such as SSRs, SNPs, InDels, etc. Among all these markers, microsatellite SSR markers can be mined from the ddRADseq data as certain properties of SSR markers make them ideal markers for study. These assist researchers and breeders in diversity analysis and producing new varieties with desired traits. To extract the markers, first, the ddRADseq data is assembled into consensus sequences using STACKS program which are further assembled for mining microsatellites using QDD along with MISA tool.
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Liu C, Zhang M, Zhao X. Development of unigene-derived SSR markers from RNA-seq data of Uraria lagopodioides (Fabaceae) and their application in the genus Uraria Desv. (Fabaceae). BMC PLANT BIOLOGY 2023; 23:87. [PMID: 36759771 PMCID: PMC9912670 DOI: 10.1186/s12870-023-04086-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Uraria Desv. belongs to the tribe Desmodieae (Fabaceae), a group of legume plants, some of which have medicinal properties. However, due to a lack of genomic information, the interspecific relationships, genetic diversity, population genetics, and identification of functional genes within Uraria species are still unclear. RESULTS Using RNA-Seq, a total of 66,026 Uraria lagopodioides unigenes with a total sequence content of 52,171,904 bp were obtained via de novo assembly and annotated using GO, KEGG, and KOG databases. 17,740 SSRs were identified from a set of 66,026 unigenes. Cross-species amplification showed that 54 out of 150 potential unigene-derived SSRs were transferable in Uraria, of which 19 polymorphic SSRs were developed. Cluster analysis based on polymorphisms successfully distinguished seven Uraria species and revealed their interspecific relationships. Seventeen samples of seven Uraria species were clustered into two monophyletic clades, and phylogenetic relationships of Uraria species based on unigene-derived SSRs were consistent with classifications based on morphological characteristics. CONCLUSIONS Unigenes annotated in the present study will provide new insights into the functional genomics of Uraria species. Meanwhile, the unigene-derived SSR markers developed here will be invaluable for assessing the genetic diversity and evolutionary history of Uraria and relatives.
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Affiliation(s)
- Chaoyu Liu
- College of Forestry, Southwest Forestry University, Kunming, 650224, China
| | - Maomao Zhang
- College of Forestry, Southwest Forestry University, Kunming, 650224, China
| | - Xueli Zhao
- College of Forestry, Southwest Forestry University, Kunming, 650224, China.
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Southwest China, Southwest Forestry University, Kunming, 650224, China.
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12
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Xiang N, Lu B, Yuan T, Yang T, Guo J, Wu Z, Liu H, Liu X, Qin R. De Novo Transcriptome Assembly and EST-SSR Marker Development and Application in Chrysosplenium macrophyllum. Genes (Basel) 2023; 14:genes14020279. [PMID: 36833206 PMCID: PMC9956384 DOI: 10.3390/genes14020279] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
Chrysosplenium macrophyllum Oliv., belonging to the family Saxifragaceae, is a traditional and unique Chinese herbal medicine. However, the lack of adequate molecular markers has hampered the progress regarding population genetics and evolution within this species. In this research, we used the DNBSEQ-T7 Sequencer (MGI) sequencing assay to analyze the transcriptome profiles of C. macrophyllum. SSR markers were developed on the basis of transcriptomic sequences and further validated on C. macrophyllum and other Chrysosplenium species. The genetic diversity and structure of the 12 populations were analyzed by using polymorphic expressed sequence tag simple sequence repeat (EST-SSR) markers. A potential pool of 3127 non-redundant EST-SSR markers were identified for C. macrophyllum in this study. The developed EST-SSR markers had high amplification rates and cross-species transferability in Chrysosplenium. Our results also showed that the natural populations of C. macrophyllum had a high level of genetic diversity. Genetic distance, principal component analysis, and popular structure analysis revealed that all 60 samples clustered into two major groups that were consistent with their geographical origins. This study provided a batch of highly polymorphic EST-SSR molecular markers that were developed via transcriptome sequencing. These markers will be of great significance for the study of the genetic diversity and evolutionary history of C. macrophyllum and other Chrysosplenium species.
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Affiliation(s)
- Niyan Xiang
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa 850000, China
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Bojie Lu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Tao Yuan
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa 850000, China
| | - Tiange Yang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Jiani Guo
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa 850000, China
| | - Zhihua Wu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Xing Liu
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa 850000, China
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Correspondence: (X.L.); (R.Q.)
| | - Rui Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
- Correspondence: (X.L.); (R.Q.)
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Zhu Y, Zhang X, Yan S, Feng C, Wang D, Yang W, Daud MK, Xiang J, Mei L. SSR identification and phylogenetic analysis in four plant species based on complete chloroplast genome sequences. Plasmid 2023; 125:102670. [PMID: 36828204 DOI: 10.1016/j.plasmid.2023.102670] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023]
Abstract
The effective utilization of traditional Chinese medicine (TCM) has been challenged by the difficulty to accurately distinguish between similar plant varieties. The stability and conservation of the chloroplast genome can aid in resolving genotypes. Previous studies using nuclear sequences and molecular markers have not effectively differentiated the species from related taxa, such as Machilus leptophylla, Hanceola exserta, Rubus bambusarum, and Rubus henryi. This study aimed to characterize the chloroplast genomes of these four plant species, and analyze their simple sequence repeats (SSRs) and phylogenetic positions. The results demonstrated the four chloroplast genomes consisted of 152.624 kb, 153.296 kb, 156.309 kb, and 158.953 kb in length, involving 124, 130, 129, and 131 genes, respectively. They also contained four specific regions with mononucleotide being the class with the most members. Moreover, these repeating types of SSR were various in individual class. Phylogenetic analysis showed that M. leptophylla was clustered with M. yunnanensis, and H. exserta was confirmed as belonging to the family Ocimeae. Additionally, R. bambusarum and R. henryi were grouped together but differed in their SSR features, indicating that they were not the same species. This research provides evidence for resolving species and contributes new genetic information for further studies.
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Affiliation(s)
- Yueyi Zhu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xianwen Zhang
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Shufeng Yan
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Chen Feng
- Lushan Botanical Garden, Chinese Academy of Sciences, Lushan 330000, China
| | - Dongfang Wang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Wei Yang
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, China
| | - Muhammad Khan Daud
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat 26000, Pakistan
| | - Jiqian Xiang
- Enshi Tujia & Miao Autonomous Prefecture Academy of Agricultural Sciences, Enshi 445000, China
| | - Lei Mei
- Enshi Tujia & Miao Autonomous Prefecture Academy of Agricultural Sciences, Enshi 445000, China; Center of Research and Development, Senium Science Development (Zhejiang) Company Limited, Hangzhou 311121, China.
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Wang Y, Xu J, Zhao W, Li J, Chen J. Genome-wide identification, characterization, and genetic diversity of CCR gene family in Dalbergia odorifera. FRONTIERS IN PLANT SCIENCE 2022; 13:1064262. [PMID: 36600926 PMCID: PMC9806228 DOI: 10.3389/fpls.2022.1064262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Lignin is a complex aromatic polymer plays major biological roles in maintaining the structure of plants and in defending them against biotic and abiotic stresses. Cinnamoyl-CoA reductase (CCR) is the first enzyme in the lignin-specific biosynthetic pathway, catalyzing the conversion of hydroxycinnamoyl-CoA into hydroxy cinnamaldehyde. Dalbergia odorifera T. Chen is a rare rosewood species for furniture, crafts and medicine. However, the CCR family genes in D. odorifera have not been identified, and their function in lignin biosynthesis remain uncertain. METHODS AND RESULTS Here, a total of 24 genes, with their complete domains were identified. Detailed sequence characterization and multiple sequence alignment revealed that the DoCCR protein sequences were relatively conserved. They were divided into three subfamilies and were unevenly distributed on 10 chromosomes. Phylogenetic analysis showed that seven DoCCRs were grouped together with functionally characterized CCRs of dicotyledons involved in developmental lignification. Synteny analysis showed that segmental and tandem duplications were crucial in the expansion of CCR family in D. odorifera, and purifying selection emerged as the main force driving these genes evolution. Cis-acting elements in the putative promoter regions of DoCCRs were mainly associated with stress, light, hormones, and growth/development. Further, analysis of expression profiles from the RNA-seq data showed distinct expression patterns of DoCCRs among different tissues and organs, as well as in response to stem wounding. Additionally, 74 simple sequence repeats (SSRs) were identified within 19 DoCCRs, located in the intron or untranslated regions (UTRs), and mononucleotide predominated. A pair of primers with high polymorphism and good interspecific generality was successfully developed from these SSRs, and 7 alleles were amplified in 105 wild D. odorifera trees from 17 areas covering its whole native distribution. DISCUSSION Overall, this study provides a basis for further functional dissection of CCR gene families, as well as breeding improvement for wood properties and stress resistance in D. odorifera.
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Affiliation(s)
- Yue Wang
- Hainan Yazhou Bay Seed Laboratory, School of Forestry, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
| | - Jieru Xu
- Hainan Yazhou Bay Seed Laboratory, School of Forestry, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
| | - Wenxiu Zhao
- Hainan Yazhou Bay Seed Laboratory, School of Forestry, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
| | - Jia Li
- Hainan Yazhou Bay Seed Laboratory, School of Forestry, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
| | - Jinhui Chen
- Hainan Yazhou Bay Seed Laboratory, School of Forestry, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
- Research Institute of Forestry, Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, China
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15
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Antunes AM, Nunes Stival JG, Targueta CP, de Campos Telles MP, Soares TN. A Pipeline for the Development of Microsatellite Markers using Next Generation Sequencing Data. Curr Genomics 2022; 23:175-181. [PMID: 36777003 PMCID: PMC9878831 DOI: 10.2174/1389202923666220428101350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/27/2022] [Accepted: 02/14/2022] [Indexed: 11/22/2022] Open
Abstract
Background: Also known as Simple Sequence Repetitions (SSRs), microsatellites are profoundly informative molecular markers and powerful tools in genetics and ecology studies on plants. Objective: This research presents a workflow for developing microsatellite markers using genome skimming. Methods: The pipeline was proposed in several stages that must be performed sequentially: obtaining DNA sequences, identifying microsatellite regions, designing primers, and selecting candidate microsatellite regions to develop the markers. Our pipeline efficiency was analyzed using Illumina sequencing data from the non-model tree species Pterodon emarginatus Vog. Results: The pipeline revealed 4,382 microsatellite regions and drew 7,411 pairs of primers for P. emarginatus. However, a much larger number of microsatellite regions with the potential to develop markers were discovered from our pipeline. We selected 50 microsatellite regions with high potential for developing markers and organized 29 microsatellite regions in sets for multiplex PCR. Conclusion: The proposed pipeline is a powerful tool for fast and efficient development of microsatellite markers on a large scale in several species, especially nonmodel plant species.
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Affiliation(s)
- Adriana Maria Antunes
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brasil;,Programa de Pós Graduação em Genética e Melhoramento de Plantas, Escola de Agronomia, Universidade Federal de Goias, Goiânia, Goiás, Brasil;,Address correspondence to this author at the Department of Genetics, Institute of Biological Sciences, Goias Federal University, Goiânia, Brazil; Tel/Fax: +55 62 981660987; E-mail:
| | - Júlio Gabriel Nunes Stival
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brasil
| | - Cíntia Pelegrineti Targueta
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brasil
| | - Mariana Pires de Campos Telles
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brasil;,Escola de Ciências Médicas e da Vida, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brasil
| | - Thannya Nascimentos Soares
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brasil;,Programa de Pós Graduação em Genética e Melhoramento de Plantas, Escola de Agronomia, Universidade Federal de Goias, Goiânia, Goiás, Brasil
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16
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The Diversity of Melia azedarach L. from China Based on Transcriptome-Developed SSR Marker. FORESTS 2022. [DOI: 10.3390/f13071011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Melia azedarach L. is a native tree species that can be used in a comprehensive way and is widely distributed in all provinces south of the Yellow River in China. Genetic diversity analysis of different M. azedarach germplasm sources is an important basic work for the selection, evaluation, and genetic improvement of M. azedarach germplasm resources. In this study, 100 pairs of SSR primers were designed and synthesized based on M. azedarach transcriptome data, and 16 pairs of reliable SSR primers were finally selected. The developed primers were used to analyze the genetic diversity of M. azedarach from 15 sources in 10 provinces in East, Central, and South China. The results showed that the frequency of the M. azedarach transcriptome SSR loci was high, and the distribution density was high. There were 15 sources of M. azedarach genetic diversity at a moderate level, and genetic variation was mainly present within the sources. The present study further enriches the existing SSR marker database of the M. azedarach family and can provide a reference for genetic diversity analysis and molecularly assisted breeding of M. azedarach plants at the genomic level.
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17
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The Landscape of Genome-Wide and Gender-Specific Microsatellites in Indo-Pacific Humpback Dolphin and Potential Applications in Cetacean Resource Investigation. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10060834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Microsatellites are one of the important genome characterizations that can be a valuable resource for variety identification, genetic diversity, phylogenetic analysis, as well as comparative and conservation genomics research. Here, we developed comprehensive microsatellites through genome-wide mining for the threatened cetacean Indo-Pacific humpback dolphin (Sousa chinensis). We found 87,757 microsatellites with 2–6 bp nucleotide motifs, showing that about 32.5 microsatellites per megabase comprises microsatellites sequences. Approximately 97.8% of the markers developed in this study were consistent with the published identified markers. About 75.3% microsatellites were with dinucleotide motifs, followed by tetranucleotide motifs (17.4%), sharing the same composition pattern as other cetaceans. The microsatellites were not evenly distributed in the S. chinensis genome, mainly in non-coding regions, with only about 0.5% of the markers located in coding regions. The microsatellite-containing genes were mainly functionally enriched in the methylation process, probably demonstrating the potential impacts of microsatellites on biological functions. Polymorphic microsatellites were developed between different genders of S. chinensis, which was expected to lay the foundation for genetic diversity investigation in cetaceans. The specific markers for a male Indo-Pacific humpback dolphin will provide comprehensive and representative male candidate markers for sex identification, providing a potential biomolecular tool for further analysis of population structure and social behavior of wild populations, population trend evaluation, and species conservation management.
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Zhou Z, Zhang L, Shu J, Wang M, Li H, Shu H, Wang X, Sun Q, Zhang S. Root Breeding in the Post-Genomics Era: From Concept to Practice in Apple. PLANTS (BASEL, SWITZERLAND) 2022; 11:1408. [PMID: 35684181 PMCID: PMC9182997 DOI: 10.3390/plants11111408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/05/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
The development of rootstocks with a high-quality dwarf-type root system is a popular research topic in the apple industry. However, the precise breeding of rootstocks is still challenging, mainly because the root system is buried deep underground, roots have a complex life cycle, and research on root architecture has progressed slowly. This paper describes ideas for the precise breeding and domestication of wild apple resources and the application of key genes. The primary goal of this research is to combine the existing rootstock resources with molecular breeding and summarize the methods of precision breeding. Here, we reviewed the existing rootstock germplasm, high-quality genome, and genetic resources available to explain how wild resources might be used in modern breeding. In particular, we proposed the 'from genotype to phenotype' theory and summarized the difficulties in future breeding processes. Lastly, the genetics governing root diversity and associated regulatory mechanisms were elaborated on to optimize the precise breeding of rootstocks.
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Affiliation(s)
- Zhou Zhou
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Lei Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Jing Shu
- College of Forestry Engineering, Shandong Agriculture and Engineering University, Jinan 250100, China;
| | - Mengyu Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Han Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Huairui Shu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Xiaoyun Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Qinghua Sun
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
| | - Shizhong Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (Z.Z.); (L.Z.); (M.W.); (H.L.); (H.S.); (X.W.)
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Dynamic Changes in Ascorbic Acid Content during Fruit Development and Ripening of Actinidia latifolia (an Ascorbate-Rich Fruit Crop) and the Associated Molecular Mechanisms. Int J Mol Sci 2022; 23:ijms23105808. [PMID: 35628618 PMCID: PMC9146223 DOI: 10.3390/ijms23105808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/13/2022] [Accepted: 05/20/2022] [Indexed: 11/16/2022] Open
Abstract
Actinidia latifolia is one of the very few kiwifruit genotypes with extremely high ascorbic acid (AsA) content. However, a transcriptome atlas of this species is lacking. The accumulation of AsA during fruit development and ripening and the associated molecular mechanisms are still poorly understood. Herein, dynamic changes in AsA content at six different stages of A. latifolia fruit development and ripening were determined. AsA content of A. latifolia fruit reached 1108.76 ± 35.26 mg 100 g−1 FW at full maturity. A high-quality, full-length (FL) transcriptome of A. latifolia was successfully constructed for the first time using third-generation sequencing technology. The transcriptome comprises 326,926 FL non-chimeric reads, 15,505 coding sequences, 2882 transcription factors, 18,797 simple sequence repeats, 3328 long noncoding RNAs, and 231 alternative splicing events. The genes involved in AsA biosynthesis and recycling pathways were identified and compared with those in different kiwifruit genotypes. The correlation between the AsA content and expression levels of key genes in AsA biosynthesis and recycling pathways was revealed. LncRNAs that participate in AsA-related gene expression regulation were also identified. Gene expression patterns in AsA biosynthesis and metabolism exhibited a trend similar to that of AsA accumulation. Overall, this study paves the way for genetic engineering to develop kiwifruits with super-high AsA content.
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Zwyrtková J, Blavet N, Doležalová A, Cápal P, Said M, Molnár I, Vrána J, Doležel J, Hřibová E. Draft Sequencing Crested Wheatgrass Chromosomes Identified Evolutionary Structural Changes and Genes and Facilitated the Development of SSR Markers. Int J Mol Sci 2022; 23:ijms23063191. [PMID: 35328613 PMCID: PMC8948999 DOI: 10.3390/ijms23063191] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/13/2022] [Accepted: 03/14/2022] [Indexed: 02/01/2023] Open
Abstract
Crested wheatgrass (Agropyron cristatum), a wild relative of wheat, is an attractive source of genes and alleles for their improvement. Its wider use is hampered by limited knowledge of its complex genome. In this work, individual chromosomes were purified by flow sorting, and DNA shotgun sequencing was performed. The annotation of chromosome-specific sequences characterized the DNA-repeat content and led to the identification of genic sequences. Among them, genic sequences homologous to genes conferring plant disease resistance and involved in plant tolerance to biotic and abiotic stress were identified. Genes belonging to the important groups for breeders involved in different functional categories were found. The analysis of the DNA-repeat content identified a new LTR element, Agrocen, which is enriched in centromeric regions. The colocalization of the element with the centromeric histone H3 variant CENH3 suggested its functional role in the grass centromere. Finally, 159 polymorphic simple-sequence-repeat (SSR) markers were identified, with 72 of them being chromosome- or chromosome-arm-specific, 16 mapping to more than one chromosome, and 71 mapping to all the Agropyron chromosomes. The markers were used to characterize orthologous relationships between A. cristatum and common wheat that will facilitate the introgression breeding of wheat using A. cristatum.
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Wang H, Gao S, Liu Y, Wang P, Zhang Z, Chen D. A pipeline for effectively developing highly polymorphic simple sequence repeats markers based on multi‐sample genomic data. Ecol Evol 2022; 12:e8705. [PMID: 35342577 PMCID: PMC8928897 DOI: 10.1002/ece3.8705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 01/25/2022] [Accepted: 02/15/2022] [Indexed: 01/24/2023] Open
Abstract
Simple sequence repeats (SSRs) are widely used genetic markers in ecology, evolution, and conservation even in the genomics era, while a general limitation to their application is the difficulty of developing polymorphic SSR markers. Next‐generation sequencing (NGS) offers the opportunity for the rapid development of SSRs; however, previous studies developing SSRs using genomic data from only one individual need redundant experiments to test the polymorphisms of SSRs. In this study, we designed a pipeline for the rapid development of polymorphic SSR markers from multi‐sample genomic data. We used bioinformatic software to genotype multiple individuals using resequencing data, detected highly polymorphic SSRs prior to experimental validation, significantly improved the efficiency and reduced the experimental effort. The pipeline was successfully applied to a globally threatened species, the brown eared‐pheasant (Crossoptilon mantchuricum), which showed very low genomic diversity. The 20 newly developed SSR markers were highly polymorphic, the average number of alleles was much higher than the genomic average. We also evaluated the effect of the number of individuals and sequencing depth on the SSR mining results, and we found that 10 individuals and ~10X sequencing data were enough to obtain a sufficient number of polymorphic SSRs, even for species with low genetic diversity. Furthermore, the genome assembly of NGS data from the optimal number of individuals and sequencing depth can be used as an alternative reference genome if a high‐quality genome is not available. Our pipeline provided a paradigm for the application of NGS technology to mining and developing molecular markers for ecological and evolutionary studies.
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Affiliation(s)
- Hui Wang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering College of Life Sciences Beijing Normal University Beijing China
| | - Shenghan Gao
- State Key Laboratory of Microbial Resources Institute of Microbiology Chinese Academy of Sciences Beijing China
| | - Yu Liu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering College of Life Sciences Beijing Normal University Beijing China
| | - Pengcheng Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology College of Life Sciences Nanjing Normal University Nanjing China
| | - Zhengwang Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering College of Life Sciences Beijing Normal University Beijing China
| | - De Chen
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering College of Life Sciences Beijing Normal University Beijing China
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Evolutionary Genetics of Cacti: Research Biases, Advances and Prospects. Genes (Basel) 2022; 13:genes13030452. [PMID: 35328006 PMCID: PMC8952820 DOI: 10.3390/genes13030452] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/22/2022] [Accepted: 02/25/2022] [Indexed: 02/01/2023] Open
Abstract
Here, we present a review of the studies of evolutionary genetics (phylogenetics, population genetics, and phylogeography) using genetic data as well as genome scale assemblies in Cactaceae (Caryophyllales, Angiosperms), a major lineage of succulent plants with astonishing diversity on the American continent. To this end, we performed a literature survey (1992–2021) to obtain detailed information regarding key aspects of studies investigating cactus evolution. Specifically, we summarize the advances in the following aspects: molecular markers, species delimitation, phylogenetics, hybridization, biogeography, and genome assemblies. In brief, we observed substantial growth in the studies conducted with molecular markers in the past two decades. However, we found biases in taxonomic/geographic sampling and the use of traditional markers and statistical approaches. We discuss some methodological and social challenges for engaging the cactus community in genomic research. We also stressed the importance of integrative approaches, coalescent methods, and international collaboration to advance the understanding of cactus evolution.
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Chen J, Li F, Wang M, Li J, Marquez-Lago TT, Leier A, Revote J, Li S, Liu Q, Song J. BigFiRSt: A Software Program Using Big Data Technique for Mining Simple Sequence Repeats From Large-Scale Sequencing Data. Front Big Data 2022; 4:727216. [PMID: 35118375 PMCID: PMC8805145 DOI: 10.3389/fdata.2021.727216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 12/13/2021] [Indexed: 11/22/2022] Open
Abstract
Background Simple Sequence Repeats (SSRs) are short tandem repeats of nucleotide sequences. It has been shown that SSRs are associated with human diseases and are of medical relevance. Accordingly, a variety of computational methods have been proposed to mine SSRs from genomes. Conventional methods rely on a high-quality complete genome to identify SSRs. However, the sequenced genome often misses several highly repetitive regions. Moreover, many non-model species have no entire genomes. With the recent advances of next-generation sequencing (NGS) techniques, large-scale sequence reads for any species can be rapidly generated using NGS. In this context, a number of methods have been proposed to identify thousands of SSR loci within large amounts of reads for non-model species. While the most commonly used NGS platforms (e.g., Illumina platform) on the market generally provide short paired-end reads, merging overlapping paired-end reads has become a common way prior to the identification of SSR loci. This has posed a big data analysis challenge for traditional stand-alone tools to merge short read pairs and identify SSRs from large-scale data. Results In this study, we present a new Hadoop-based software program, termed BigFiRSt, to address this problem using cutting-edge big data technology. BigFiRSt consists of two major modules, BigFLASH and BigPERF, implemented based on two state-of-the-art stand-alone tools, FLASH and PERF, respectively. BigFLASH and BigPERF address the problem of merging short read pairs and mining SSRs in the big data manner, respectively. Comprehensive benchmarking experiments show that BigFiRSt can dramatically reduce the execution times of fast read pairs merging and SSRs mining from very large-scale DNA sequence data. Conclusions The excellent performance of BigFiRSt mainly resorts to the Big Data Hadoop technology to merge read pairs and mine SSRs in parallel and distributed computing on clusters. We anticipate BigFiRSt will be a valuable tool in the coming biological Big Data era.
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Affiliation(s)
- Jinxiang Chen
- Department of Software Engineering, College of Information Engineering, Northwest A&F University, Yangling, China
| | - Fuyi Li
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
- Monash Centre for Data Science, Monash University, Melbourne, VIC, Australia
- Department of Microbiology and Immunity, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Miao Wang
- Department of Software Engineering, College of Information Engineering, Northwest A&F University, Yangling, China
| | - Junlong Li
- Department of Software Engineering, College of Information Engineering, Northwest A&F University, Yangling, China
| | - Tatiana T. Marquez-Lago
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - André Leier
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jerico Revote
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Shuqin Li
- Department of Software Engineering, College of Information Engineering, Northwest A&F University, Yangling, China
| | - Quanzhong Liu
- Department of Software Engineering, College of Information Engineering, Northwest A&F University, Yangling, China
- Quanzhong Liu
| | - Jiangning Song
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
- Monash Centre for Data Science, Monash University, Melbourne, VIC, Australia
- *Correspondence: Jiangning Song
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Genome survey sequencing and characterization of simple sequence repeat (SSR) markers in Platostoma palustre (Blume) A.J.Paton (Chinese mesona). Sci Rep 2022; 12:355. [PMID: 35013469 PMCID: PMC8748427 DOI: 10.1038/s41598-021-04264-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 11/30/2021] [Indexed: 12/25/2022] Open
Abstract
Platostoma palustre (Blume) A.J.Paton is an annual herbaceous persistent plant of the Labiatae family. However, there is a lack of genomic data for this plant, which severely restricts its genetic improvement. In this study, we performed genome survey sequencing of P. palustre and developed simple sequence repeat (SSR) markers based on the resulting sequence. K-mer analysis revealed that the assembled genome size was approximately 1.21 Gb. A total of 15,498 SSR motifs were identified and characterized in this study; among them, dinucleotide, and hexanucleotide repeats had the highest and lowest, respectively. Among the dinucleotide repeat motifs, AT/TA repeat motifs were the most abundant, and GC/CG repeat motifs were rather rare, accounting for 44.28% and 0.63%, respectively. Genetic similarity coefficient analysis by the UPMGA methods clustered 12 clones, of P. palustre and related species into two subgroups. These results provide helpful information for further research on P. palustre resources and variety improvements.
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Adolfo LM, Rao X, Dixon RA. Identification of Pueraria spp. through DNA barcoding and comparative transcriptomics. BMC PLANT BIOLOGY 2022; 22:10. [PMID: 34979934 PMCID: PMC8722073 DOI: 10.1186/s12870-021-03383-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 12/05/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Kudzu is a term used generically to describe members of the genus Pueraria. Kudzu roots have been used for centuries in traditional Chinese medicine in view of their high levels of beneficial isoflavones including the unique 8-C-glycoside of daidzein, puerarin. In the US, kudzu is seen as a noxious weed causing ecological and economic damage. However, not all kudzu species make puerarin or are equally invasive. Kudzu remains difficult to identify due to its diverse morphology and inconsistent nomenclature. RESULTS We have generated sequences for the internal transcribed spacer 2 (ITS2) and maturase K (matK) regions of Pueraria montana lobata, P. montana montana, and P. phaseoloides, and identified two accessions previously used for differential analysis of puerarin biosynthesis as P. lobata and P. phaseoloides. Additionally, we have generated root transcriptomes for the puerarin-producing P. m. lobata and the non-puerarin producing P. phaseoloides. Within the transcriptomes, microsatellites were identified to aid in species identification as well as population diversity. CONCLUSIONS The barcode sequences generated will aid in fast and efficient identification of the three kudzu species. Additionally, the microsatellites identified from the transcriptomes will aid in genetic analysis. The root transcriptomes also provide a molecular toolkit for comparative gene expression analysis towards elucidation of the biosynthesis of kudzu phytochemicals.
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Affiliation(s)
- Laci M Adolfo
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203-5017, USA
| | - Xiaolan Rao
- College of Life Sciences, Hubei University, Wuhan, 430068, Hubei Province, China
| | - Richard A Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203-5017, USA.
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Analysis of SSR and SNP markers. Bioinformatics 2022. [DOI: 10.1016/b978-0-323-89775-4.00017-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Melo PZ, Antunes AM, Fernandes JG, Targueta CP, Guimarães RA, Boaventura-Novaes CRD, Soares TN. Development of microsatellite markers in Pterodon pubescens and transferability to Pterodon emarginatus, two Brazilian plant species with medicinal potential. RODRIGUÉSIA 2022. [DOI: 10.1590/2175-7860202273091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Abstract Pterodon pubescens and P. emarginatus (Leguminosae) are native medicinal plants of Brazil. Extractivism due to its therapeutic properties threatens populations of both species. Studies of genetic diversity is a way to reason the use and promote conservation. We developed microsatellite markers for P. pubescens and transferred them to P. emarginatus to further genetic diversity investigation of these species. From genomic sequences of P. pubescens, obtained via the Illumina MiSeq platform, it was possible to identify 6,514 microsatellite regions, to design 5,419 primer pairs, and to test 30 markers amplification. We provide 26 polymorphic microsatellite markers, 10 of which were genotyped in 48 individuals per species. The number of alleles per locus range from 3 to 16, with high average genetic diversity ( P. pubescens HE = 0.753; P. emarginatus HE = 0.691). The genotyped markers have a high paternity exclusion probability (Q values greater than 0.99) and low probability of identity, indicating that set of loci is capable of individual discriminating in P. pubescens and P. emarginatus. Microsatellite markers provided in this study are a tool for population genetics studies and conservation of the two species and can be applied to closely related non-model species.
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Affiliation(s)
- Priscila Zei Melo
- Universidade Federal de Goiás, Brazil; Universidade Federal de Goiás, Brazil
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Xu Y, Xing M, Song L, Yan J, Lu W, Zeng A. Genome-Wide Analysis of Simple Sequence Repeats in Cabbage ( Brassica oleracea L.). FRONTIERS IN PLANT SCIENCE 2021; 12:726084. [PMID: 34956251 PMCID: PMC8695497 DOI: 10.3389/fpls.2021.726084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
Cabbage (Brassica oleracea L. var. capitata) accounts for a critical vegetable crop belonging to Brassicaceae family, and it has been extensively planted worldwide. Simple sequence repeats (SSRs), the markers with high polymorphism and co-dominance degrees, offer a crucial genetic research resource. The current work identified totally 64,546 perfect and 93,724 imperfect SSR motifs in the genome of the cabbage 'TO1000.' Then, we divided SSRs based on the respective overall length and repeat number into different linkage groups. Later, we characterized cabbage genomes from the perspectives of motif length, motif-type classified and SSR level, and compared them across cruciferous genomes. Furthermore, a large set of 64,546 primer pairs were successfully identified, which generated altogether 1,113 SSR primers, including 916 (82.3%) exhibiting repeated and stable amplification. In addition, there were 32 informative SSR markers screened, which might decide 32 cabbage genotypes for their genetic diversity, with level of polymorphism information of 0.14-0.88. Cultivars were efficiently identified by the new strategy designating manual diagram for identifying cultivars. Lastly, 32 cabbage accessions were clearly separately by five Bol-SSR markers. Besides, we verified whether such SSRs were available and transferable in 10 Brassicaceae relatives. Based on the above findings, those genomic SSR markers identified in the present work may facilitate cabbage research, which lay a certain foundation for further gene tagging and genetic linkage analyses, like marker-assisted selection, genetic mapping, as well as comparative genomic analysis.
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Liu H, Zhang Y, Wang Z, Su Y, Wang T. Development and Application of EST-SSR Markers in Cephalotaxus oliveri From Transcriptome Sequences. Front Genet 2021; 12:759557. [PMID: 34868238 PMCID: PMC8635753 DOI: 10.3389/fgene.2021.759557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
Cephalotaxus oliveri is an endemic conifer of China, which has medicinal and ornamental value. However, the limited molecular markers and genetic information are insufficient for further genetic studies of this species. In this study, we characterized and developed the EST-SSRs from transcriptome sequences for the first time. The results showed that a total of 5089 SSRs were identified from 36446 unigenes with a density of one SSR per 11.1 kb. The most common type was trinucleotide repeats, excluding mononucleotide repeats, followed by dinucleotide repeats. AAG/CTT and AT/AT exhibited the highest frequency in the trinucleotide and dinucleotide repeats, respectively. Of the identified SSRs, 671, 1125, and 1958 SSRs were located in CDS, 3′UTR, and 5′UTR, respectively. Functional annotation showed that the SSR-containing unigenes were involved in growth and development with various biological functions. Among successfully designed primer pairs, 238 primer pairs were randomly selected for amplification and validation of EST-SSR markers and 47 primer pairs were identified as polymorphic. Finally, 28 high-polymorphic primers were used for genetic analysis and revealed a moderate level of genetic diversity. Seven natural C. oliveri sampling sites were divided into two genetic groups. Furthermore, the 28 EST-SSRs had 96.43, 71.43, and 78.57% of transferability rate in Cephalotaxus fortune, Ametotaxus argotaenia, and Pseudotaxus chienii, respectively. These markers developed in this study lay the foundation for further genetic and adaptive evolution studies in C. oliveri and related species.
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Affiliation(s)
- Hanjing Liu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuli Zhang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhen Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, China
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, China
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30
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Development of InDel markers and establishment of a specific molecular marker of the new strain (SW-81) in Pyropia haitanensis. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Choi H, Kang WS, Kim JS, Na CS, Kim S. De Novo Assembly and Species-Specific Marker Development as a Useful Tool for the Identification of Scutellaria L. Species. Curr Issues Mol Biol 2021; 43:2177-2188. [PMID: 34940126 PMCID: PMC8929090 DOI: 10.3390/cimb43030152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/17/2021] [Accepted: 11/29/2021] [Indexed: 12/04/2022] Open
Abstract
Scutellaria L. (family Lamiaceae) includes approximately 470 species found in most parts of the world and is commonly known as skullcaps. Scutellaria L. is a medicinal herb used as a folk remedy in Korea and East Asia, but it is difficult to identify and classify various subspecies by morphological methods. Since Scutellaria L. has not been studied genetically, to expand the knowledge of species in the genus Scutellaria L., de novo whole-genome assembly was performed in Scutellaria indica var. tsusimensis (H. Hara) Ohwi using the Illumina sequencing platform. We aimed to develop a molecular method that could be used to classify S.indica var. tsusimensis (H. Hara) Ohwi, S. indica L. and three other Scutellaria L. species. The assembly results for S.indica var. tsusimensis (H. Hara) Ohwi revealed a genome size of 318,741,328 bp and a scaffold N50 of 78,430. The assembly contained 92.08% of the conserved BUSCO core gene set and was estimated to cover 94.65% of the genome. The obtained genes were compared with previously registered Scutellaria nucleotide sequences and similar regions using the NCBI BLAST service, and a total of 279 similar nucleotide sequences were detected. By selecting the 279 similar nucleotide sequences and nine chloroplast DNA barcode genes, primers were prepared so that the size of the PCR product was 100 to 1000 bp. As a result, a species-specific primer set capable of distinguishing five species of Scutellaria L. was developed.
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Affiliation(s)
- Hakjoon Choi
- Central R&D Center, B&Tech Co., Ltd., Gwangju 61239, Korea; (H.C.); (W.S.K.); (J.S.K.)
| | - Wan Seok Kang
- Central R&D Center, B&Tech Co., Ltd., Gwangju 61239, Korea; (H.C.); (W.S.K.); (J.S.K.)
| | - Jin Seok Kim
- Central R&D Center, B&Tech Co., Ltd., Gwangju 61239, Korea; (H.C.); (W.S.K.); (J.S.K.)
| | - Chang-Su Na
- College of Korean Medicine, Dongshin University, Naju-si 58245, Korea;
| | - Sunoh Kim
- Central R&D Center, B&Tech Co., Ltd., Gwangju 61239, Korea; (H.C.); (W.S.K.); (J.S.K.)
- Correspondence: ; Tel.: +82-62-528-2201; Fax: +82-62-528-2202
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Patturaj M, Munusamy A, Kannan N, Kandasamy U, Ramasamy Y. Chromosome-specific polymorphic SSR markers in tropical eucalypt species using low coverage whole genome sequences: systematic characterization and validation. Genomics Inform 2021; 19:e33. [PMID: 34638180 PMCID: PMC8510864 DOI: 10.5808/gi.21031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 06/29/2021] [Indexed: 11/20/2022] Open
Abstract
Eucalyptus is one of the major plantation species with wide variety of industrial uses. Polymorphic and informative simple sequence repeats (SSRs) have broad range of applications in genetic analysis. In this study, two individuals of Eucalyptus tereticornis (ET217 and ET86), one individual each from E. camaldulensis (EC17) and E. grandis (EG9) were subjected to whole genome resequencing. Low coverage (10×) genome sequencing was used to find polymorphic SSRs between the individuals. Average number of SSR loci identified was 95,513 and the density of SSRs per Mb was from 157.39 in EG9 to 155.08 in EC17. Among all the SSRs detected, the most abundant repeat motifs were di-nucleotide (59.6%–62.5%), followed by tri- (23.7%–27.2%), tetra- (5.2%–5.6%), penta- (5.0%–5.3%), and hexa-nucleotide (2.7%–2.9%). The predominant SSR motif units were AG/CT and AAG/TTC. Computational genome analysis predicted the SSR length variations between the individuals and identified the gene functions of SSR containing sequences. Selected subset of polymorphic markers was validated in a full-sib family of eucalypts. Additionally, genome-wide characterization of single nucleotide polymorphisms, InDels and transcriptional regulators were carried out. These variations will find their utility in genome-wide association studies as well as understanding of molecular mechanisms involved in key economic traits. The genomic resources generated in this study would provide an impetus to integrate genomics in marker-trait associations and breeding of tropical eucalypts.
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Affiliation(s)
- Maheswari Patturaj
- Institute of Forest Genetics and Tree Breeding, Coimbatore 641002, India
| | - Aiswarya Munusamy
- Institute of Forest Genetics and Tree Breeding, Coimbatore 641002, India
| | | | | | - Yasodha Ramasamy
- Institute of Forest Genetics and Tree Breeding, Coimbatore 641002, India
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Meena RK, Negi N, Uniyal N, Bhandari MS, Sharma R, Ginwal HS. Genome skimming-based STMS marker discovery and its validation in temperate hill bamboo Drepanostachyum falcatum. J Genet 2021. [DOI: 10.1007/s12041-021-01273-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Transcriptome repository of North-Western Himalayan endangered medicinal herbs: a paramount approach illuminating molecular perspective of phytoactive molecules and secondary metabolism. Mol Genet Genomics 2021; 296:1177-1202. [PMID: 34557965 DOI: 10.1007/s00438-021-01821-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/12/2021] [Indexed: 01/23/2023]
Abstract
Medicinal plants of the North-Western Himalayan region are known for their unprecedented biodiversity and valuable secondary metabolites that are unique to this dynamic geo-climatic region. From ancient times these medicinal herbs have been used traditionally for their therapeutic potentials. But from the last 2 decades increasing pharmaceutical demand, illegal and unorganized trade of these medicinal plants have accelerated the rate of over-exploitation in a non-scientific manner. In addition, climate change and anthropogenic activities also affected their natural habitat and driving most of these endemic plant species to critically endangered that foresee peril of mass extinction from this eco-region. Hence there is an urgent need for developing alternative sustainable approaches and policies to utilize this natural bioresource ensuring simultaneous conservation. Hither, arise the advent of sequencing-based transcriptomic studies significantly contributes to better understand the background of important metabolic pathways and related genes/enzymes of high-value medicinal herbs, in the absence of genomic information. The use of comparative transcriptomics in conjunction with biochemical techniques in North-Western Himalayan medicinal plants has resulted in significant advances in the identification of the molecular players involved in the production of secondary metabolic pathways over the last decade. This information could be used to further engineer metabolic pathways and breeding programs, ultimately leading to the development of in vitro systems dedicated to the production of pharmaceutically important secondary metabolites at the industrial level. Collectively, successful adoption of these approaches can certainly ensure the sustainable utilization of Himalayan bioresource by reducing the pressure on the wild population of these critically endangered medicinal herbs. This review provides novel insight as a transcriptome-based bioresource repository for the understanding of important secondary metabolic pathways genes/enzymes and metabolism of endangered high-value North-Western Himalayan medicinal herbs, so that researchers across the globe can effectively utilize this information for devising effective strategies for the production of pharmaceutically important compounds and their scale-up for sustainable usage and take a step forward in omics-based conservation genetics.
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Dabral A, Shamoon A, Meena RK, Kant R, Pandey S, Ginwal HS, Bhandari MS. Genome skimming-based simple sequence repeat (SSR) marker discovery and characterization in Grevillea robusta. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1623-1638. [PMID: 34305342 PMCID: PMC8285676 DOI: 10.1007/s12298-021-01035-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 07/01/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
Proteaceae, a largely southern hemisphere family consisting of 80 genera distributed in Australia and southern Africa as its centres of greatest diversity, also extends well in northern and southern America. Under this family, Grevillea robusta is a fast-growing species got popularity in farm and avenue plantations. Despite the ecological and economic importance, the species has not yet been investigated for its genetic improvement and genome-based studies. Only a few molecular markers are available for the species or its close relatives, which hinders genomic and population genetics studies. Genetic markers have been intensively applied for the main strategies in breeding programs, especially for the economically important traits. Hence, it is of utmost priority to develop genomic database resources and species-specific markers for studying quantitative genetics in G. robusta. Given this, the present study aimed to develop de novo genome sequencing, robust microsatellites markers, sequence annotation and their validation in different stands of G. robusta in northern India. Library preparation and sequencing were carried out using Illumina paired-end sequencing technology. Approximately, ten gigabases (Gb) sequence data with 70.87 million raw reads assembled into 425,923 contigs (read mapped to 76.48%) comprising 455 Mb genome size (23 × coverage) generated through genome skimming approach. In total, 9421 simple sequence repeat (SSR) primer pairs were successfully designed from 13,335 microsatellite repeats. Afterward, a subset of 161 primer pairs was randomly selected, synthesized and validated. All the tested primers showed successful amplification but only 13 showed polymorphisms. The polymorphic SSRs were further used to estimate the measures of genetic diversity in 12 genotypes each from the states of Punjab, Haryana, Himachal Pradesh and Uttarakhand. Importantly, the average number of alleles (Na), observed heterozygosity (Ho), expected heterozygosity (He), and the polymorphism information content (PIC) were recorded as 2.69, 0.356, 0.557 and 0.388, respectively. The availability of sequence information and newly developed SSR markers could potentially be used in various genetic analyses and improvements through molecular breeding strategies for G. robusta. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01035-w.
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Affiliation(s)
- Aman Dabral
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand 248 195 India
| | - Arzoo Shamoon
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand 248 195 India
| | - Rajendra K. Meena
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand 248 195 India
| | - Rama Kant
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand 248 195 India
| | - Shailesh Pandey
- Forest Pathology Discipline, Division of Forest Protection, Forest Research Institute, Dehradun, Uttarakhand 248 006 India
| | - Harish S. Ginwal
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand 248 195 India
| | - Maneesh S. Bhandari
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand 248 195 India
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Development, characterization, functional annotation and validation of genomic and genic-SSR markers using de novo next generation sequencing in Melia dubia Cav. 3 Biotech 2021; 11:310. [PMID: 34109095 DOI: 10.1007/s13205-021-02858-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/22/2021] [Indexed: 10/21/2022] Open
Abstract
Melia dubia Cav. (Meliaceae), a fast-growing tropical tree finds use in plywood, pulp and high-value solid wood products. To increase its productivity, we must essentially capture genetic diversity and identify genotypes with superior wood properties. This study aimed to develop novel microsatellite markers from genomic data and validate the markers in M. dubia. Direct Seq-to-SSR approach was adopted and using an in-house Perl script, 426,390 SSR markers identified. For validation, selected 151 markers, of which 50 were genomic markers chosen randomly, and 101 were genic markers identified through BLAST2GO. Amplification was observed in all loci, and 81.4% generated high-quality, reproducible amplicons of the expected size. Out of 50 genomic markers, we used ten highly polymorphic markers to assess genetic diversity among 75 genotypes from three populations. One hundred fourteen alleles were recorded, with a moderate level of diversity and a positive fixation index. Twenty-nine genic markers representing 13 enzymes showing polymorphism for wood stiffness were selected for diversity assessment of 24 genotypes (12 genotypes each with high and low-stress wave velocity). The product size ranged from 87 to 279, covering the majority of the genome. Cluster and structure analysis segregated ~ 80% of the genotypes based on the trait. This is the first report of the development of genic markers from a genomic survey and has proved efficient in differentiating genotypes based on the trait. The markers developed in this study will be useful for genetic mapping, diversity estimation, marker-assisted selection for desired traits and breeding for wood traits in M. dubia. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02858-w.
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Komaei Koma G, Şekerli M, Snelling JW, Mehlenbacher SA. New Sources of Eastern Filbert Blight Resistance and Simple Sequence Repeat Markers on Linkage Group 6 in Hazelnut ( Corylus avellana L.). FRONTIERS IN PLANT SCIENCE 2021; 12:684122. [PMID: 34194458 PMCID: PMC8238048 DOI: 10.3389/fpls.2021.684122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/17/2021] [Indexed: 06/13/2023]
Abstract
Commercial production of hazelnut (Corylus avellana) in Oregon's Willamette Valley is threatened by eastern filbert blight (EFB), a serious canker disease caused by the pyrenomycete Anisogramma anomala (Peck) E. Müller. The fungus also prevents the establishment of hazelnut orchards in eastern North America. Genetic resistance is considered the most effective way to control the disease. A high level of EFB resistance was first discovered in 'Gasaway'. This resistance is conferred by a dominant allele at a single locus on linkage group 6 (LG6). Resistance from several additional sources has been assigned to the same chromosomal region. In this study, new simple sequence repeat (SSR) markers were developed for the resistance region on LG6 and new sources of resistance were investigated. Forty-two new SSR markers were developed from four contigs in the genome sequence of 'Jefferson' hazelnut, characterized, and nine of them were placed on LG6 of the genetic map. Accessions representing 12 new sources of EFB resistance were crossed with susceptible selections resulting in 18 seedling populations. Segregation ratios in the seedling populations fit the expected 1:1 ratio for 10 sources, while one source showed an excess of resistant seedlings and another showed an excess of susceptible seedlings. Based on correlation of disease response and scores of SSR markers in the 'Gasaway' resistance region in the seedlings, eight resistance sources were assigned to LG6. Linkage maps were constructed for each progeny using SSR markers. The LG6 resistance sources include two selections (#23 and #26) from the Russian Research Institute of Forestry and Mechanization near Moscow, four selections from southern Russia, one selection (OSU 1185.126) from Crimea, one selection (OSU 533.129) from Michigan, Corylus heterophylla 'Ogyoo' from the South Korea, and the interspecific hybrid 'Estrella #1'. These new LG6 resistance sources and SSR markers should be useful in breeding new cultivars, including the pyramiding of resistance genes. For the other four resistance sources (Moscow #37, hybrid selection OSU 401.014, C. americana 'Winkler' and C. americana OSU 366.060), SSR marker scores on linkage groups 6, 7 and 2 were not correlated with disease response and merit further investigation.
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Transcriptome sequencing and microsatellite marker discovery in Ailanthus altissima (Mill.) Swingle (Simaroubaceae). Mol Biol Rep 2021; 48:2007-2023. [PMID: 33730287 DOI: 10.1007/s11033-020-05402-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/25/2020] [Indexed: 10/21/2022]
Abstract
Ailanthus altissima Swingle, is a tree species native to East Asia and has a great potential in decorative, bioenergy and industrial applications in many countries. To date, despite its commercial importance, the genomic and genetic resources available for this species are still insufficient. In this study, we characterized the transcriptome of A. altissima and developed thirteen EST-SSRs (expressed sequence tag-simple sequence repeats) based on Illumina paired-end RNA sequencing (RNA-seq). Besides, we developed ten polymorphic chloroplast microsatellite (cpSSR) markers using the available chloroplast genome of A. altissima. The transcriptome data produced 87,797 unigenes, of which 64,891 (73.91%) unigenes were successfully annotated in at least one protein database. For cpSSR markers the number of detected alleles (N) per marker varied from three at cpSSR12 to twelve at cpSSR8, the unbiased haploid diversity indices (uh) varied from 0.111 to 0.485, and haploid diversity indices (h) ranged from 0.101 to 0.444 with an average unbiased haploid diversity index (uh) of 0.274. Overall, a total of 65 different cpSSR alleles were identified at the ten loci among 165 individuals of A. altissima. The allele number per locus for EST-SSRs varied from 2.143 to 9.357, and the values of observed and expected heterozygosity ranged from 0.312 to 1.000 and 0.505 to 0.826, respectively. The molecular markers developed in this study will facilitate future genetic diversity, population structure, long distance-gene transfer and pollen-based gene flow analyses of A. altissima populations from its known distribution ranges in China focusing on planted and natural forest stands.
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Kpatènon MJ, Salako KV, Santoni S, Zekraoui L, Latreille M, Tollon-Cordet C, Mariac C, Jaligot E, Beulé T, Adéoti K. Transferability, development of simple sequence repeat (SSR) markers and application to the analysis of genetic diversity and population structure of the African fan palm (Borassus aethiopum Mart.) in Benin. BMC Genet 2020; 21:145. [PMID: 33272218 PMCID: PMC7713368 DOI: 10.1186/s12863-020-00955-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 11/17/2020] [Indexed: 02/08/2023] Open
Abstract
Background In Sub-Saharan Africa, Borassus aethiopum Mart. (African fan palm) is an important non-timber forest product-providing palm that faces multiple anthropogenic threats to its genetic diversity. However, this species is so far under-studied, which prevents its sustainable development as a resource. The present work is a first attempt at characterizing the genetic diversity and population structure of B. aethiopum across nine collection sites spanning the three climatic regions of Benin, West Africa, through the use of microsatellite markers. Results During a first phase we relied on the reported transferability of primers developed in other palm species. We find that, in disagreement with previously published results, only 22.5% of the markers tested enable amplification of B. aethiopum DNA and polymorphism detection is very low. In a second phase, we generated a B. aethiopum-specific genomic dataset through high-throughput sequencing and used it for the de novo detection of microsatellite loci. Among the primer pairs targeting these, 11 detected polymorphisms and were further used for analyzing genetic diversity. Across the nine sites, expected heterozygosity (He) ranges from 0.263 to 0.451 with an overall average of 0.354, showing a low genetic diversity. Analysis of molecular variance (AMOVA) shows that within-site variation accounts for 53% of the genetic variation. Accordingly, the low number of migrants and positive values of the fixation index (F) in sites from both the Central (Sudano-Guinean) and the Southern (Guinean) climatic regions suggest limited gene flow between sites. The global correlation between genetic and geographic distances is weak; however, our clustering analyses indicate that B. aethiopum palms from Savè (Center) are genetically more similar to those from the North than to samples from other Central sites. Conclusions In the light of our results, we discuss the use of inter-species transfer vs. de novo development of microsatellite markers in genetic diversity analyses targeting under-studied species, and suggest future applications for our molecular resources. We propose that, while prominent short-range pollen and seed dispersal in Benin explain most of our results, gene flux between the Central and Northern regions, as a result of animal and/or human migrations, might underlie the Savè discrepancy. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-020-00955-y.
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Affiliation(s)
- Mariano Joly Kpatènon
- Laboratoire de Microbiologie et de Technologie Alimentaire (LAMITA), Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin.,Biodiversité et Ecologie des Plantes (BDEP), Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin.,DIADE, Univ Montpellier, IRD, Montpellier, France
| | - Kolawolé Valère Salako
- Biodiversité et Ecologie des Plantes (BDEP), Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin.,Laboratoire de Biomathématiques et d'Estimations Forestières (LABEF), Faculté des Sciences Agronomiques, Université d'Abomey-Calavi, Cotonou, Bénin
| | - Sylvain Santoni
- AGAP, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | | | - Muriel Latreille
- AGAP, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | | | | | - Estelle Jaligot
- DIADE, Univ Montpellier, IRD, Montpellier, France.,CIRAD, UMR DIADE, Montpellier, France
| | - Thierry Beulé
- DIADE, Univ Montpellier, IRD, Montpellier, France.,CIRAD, UMR DIADE, Montpellier, France
| | - Kifouli Adéoti
- Laboratoire de Microbiologie et de Technologie Alimentaire (LAMITA), Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin. .,Biodiversité et Ecologie des Plantes (BDEP), Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin.
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Manco R, Chiaiese P, Basile B, Corrado G. Comparative analysis of genomic- and EST-SSRs in European plum ( Prunus domestica L.): implications for the diversity analysis of polyploids. 3 Biotech 2020; 10:543. [PMID: 33235823 PMCID: PMC7679426 DOI: 10.1007/s13205-020-02513-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 10/27/2020] [Indexed: 11/23/2022] Open
Abstract
Simple sequence repeats (SSRs) are among the most useful DNA markers in plant science. The aim of this study was to compare the features and usefulness of genomic SSR (gSSR) and EST-SSRs in European plum (Prunus domestica L.), an economically important, hexaploid stone fruit crop globally cultivated to produce fleshy fruits and derived foodstuff. The analysis of an ample set of morphologically diverse varieties indicated that gSSRs and EST-SSRs provide different estimates of some of the locus-based indicators of diversity. Moreover, the two classes of SSRs gave different, weakly correlated, estimations of distance-based parameters with gSSRs being more powerful for discriminating purposes. The two SSR classes provide complementary information in European plum, making the contribution of EST-SSRs useful not only as non-neutral markers. The differences between SSR classes are discussed considering the neutral and non-neutral evolution, and the polyploidy and asexual propagation of the cultivated tree varieties.
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Li L, Liu H, Wen W, Huang C, Li X, Xiao S, Wu M, Shi J, Xu D. Full Transcriptome Analysis of Callus Suspension Culture System of Bletilla striata. Front Genet 2020; 11:995. [PMID: 33193583 PMCID: PMC7593603 DOI: 10.3389/fgene.2020.00995] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/05/2020] [Indexed: 12/13/2022] Open
Abstract
Background Bletilla striata has been widely used in the pharmacology industry. To effectively produce the secondary metabolites through suspension cultured cells of B. striata, it is important to exploring the full-length transcriptome data and the genes related to cell growth and chemical producing of all culture stages. We applied a combination of Real-Time Sequencing of Single Molecule (SMRT) and second-generation sequencing (SGS) to generate the complete and full-length transcriptome of B. striata suspension cultured cells. Methods The B. striata transcriptome was formed in de novo way by using PacBio isoform sequencing (Iso-Seq) on a pooled RNA sample derived from 23 samples of 10 culture stages, to explore the potential for capturing full-length transcript isoforms. All unigenes were obtained after splicing, assembling, and clustering, and corrected by the SGS results. The obtained unigenes were compared with the databases, and the functions were annotated and classified. Results and conclusions A total of 100,276 high-quality full-length transcripts were obtained, with an average length of 2530 bp and an N50 of 3302 bp. About 52% of total sequences were annotated against the Gene Ontology, 53,316 unigenes were hit by KOG annotations and divided into 26 functional categories, 80,020 unigenes were mapped by KEGG annotations and clustered into 363 pathways. Furthermore, 15,133 long-chain non-coding RNAs (lncRNAs) were detected. And 68,996 coding sequences were identified based on SSR analysis, among which 31 pairs of primers selected at random were amplified and obtained stable bands. In conclusion, our results provide new full-length transcriptome data and genetic resources for identifying growth and metabolism-related genes, which provide a solid foundation for further research on its growth regulation mechanisms and genetic engineering breeding mechanisms of B. striata.
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Affiliation(s)
- Lin Li
- Department of Cell Biology, Zunyi Medical University, Zunyi, China
| | - Houbo Liu
- Department of Cell Biology, Zunyi Medical University, Zunyi, China
| | - Weie Wen
- Department of Cell Biology, Zunyi Medical University, Zunyi, China
| | - Ceyin Huang
- Department of Cell Biology, Zunyi Medical University, Zunyi, China
| | - Xiaomei Li
- Department of Cell Biology, Zunyi Medical University, Zunyi, China
| | - Shiji Xiao
- School of Pharmacy, Zunyi Medical University, Zunyi, China
| | - Mingkai Wu
- Institute of Modern Chinese Herbal of Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Junhua Shi
- The Department of Imaging, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Delin Xu
- Department of Cell Biology, Zunyi Medical University, Zunyi, China
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Xu R, Wang Z, Su Y, Wang T. Characterization and Development of Microsatellite Markers in Pseudotaxus chienii (Taxaceae) Based on Transcriptome Sequencing. Front Genet 2020; 11:574304. [PMID: 33193679 PMCID: PMC7593448 DOI: 10.3389/fgene.2020.574304] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/21/2020] [Indexed: 12/12/2022] Open
Abstract
Pseudotaxus chienii (Taxaceae) is an endangered conifer species endemic to China. However, a lack of suitable molecular markers hinders the genomic and genetic studies on this species. Here, we characterized and developed the microsatellite markers from a newly sequenced P. chienii transcriptome. A total of 21,835 microsatellite loci were detected from 161,131 non-redundant unigene sequences, and the frequency of SSRs was 13.55%, with an average of one SSR loci per 9.18 kb. Mono-nucleotide, di-nucleotide, and tri-nucleotide were the dominant repeat types, accounting for 50.06, 13.49, and 29.39% of the total SSRs, respectively. In terms of distribution location, the coding regions (CDS) with few microsatellites and mainly consisted of tri-nucleotides. There were significant differences in the length of microsatellite among genic regions and motif types. Functional annotation showed that the unigenes containing microsatellites had a wide range of biological functions, most of which were related to basic metabolism, and a few might be involved in expression regulation of gene and response to environmental stress. In addition, 375 primer pairs were randomly selected and synthesized for the amplification and validation of microsatellite markers. Seventy-seven primer pairs were successfully amplified and 40 primer pairs were found to be polymorphic. Finally, 20 pairs of primers with high polymorphism were selected to assess the genetic diversity in four P. chienii populations. In addition, the newly developed microsatellite markers exhibited high transferability (70%) in Amentotaxus argotaenia. Our study could enable further genetic diversity analysis and functional gene mining on Taxaceae.
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Affiliation(s)
- Ruixiang Xu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhen Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, China
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, China
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Gonçalves AR, Barateli LO, de Souza UJB, Pereira AMS, Bertoni BW, Telles MPDC. Development and characterization of microsatellite markers in Stryphnodendron adstringens (Leguminosae). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:2095-2101. [PMID: 33088053 PMCID: PMC7548263 DOI: 10.1007/s12298-020-00876-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 08/03/2020] [Accepted: 08/26/2020] [Indexed: 06/11/2023]
Abstract
In this study, we report the development and characterization of 15 new microsatellite markers for Stryphnodendron adstringens (Leguminosae) in order to support future analyses of genetic diversity in populations of this species. In screening with 48 individuals from three different populations of S. adstringens, we tested the amplification of 20 microsatellite loci, of which five are not useful for population genetic studies due to the lack of polymorphisms or amplification failures. For the final set of 15 loci, the number of alleles ranged from 2 to 15, with a total of 116 alleles. The expected heterozygosity ranged from 0.1219 to 0.8965, with an average of 0.6694 per locus. The combined probability of genetic identity (PI = 8.12 × 10-15) and paternity exclusion (Q = 0.99999) estimations showed that the loci may be useful to discriminate between individuals of S. adstringens. Initial cross-amplification tests were satisfactory in three species of the genus Stryphnodendron: S. rotundifolium, S. coriaceum and S. polyphyllum. This new set of markers will be a useful tool for population genetic studies, contributing to the knowledge about the evolutionary history of S. adstringens and, additionally, correlated species.
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Affiliation(s)
- Ariany Rosa Gonçalves
- Programa de Pós-graduação em Genética e Melhoramento de Plantas, Escola de Agronomia, Universidade Federal de Goiás, Goiânia, Goiás Brazil
- Laboratório de Genética e Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás Brazil
| | - Luciana Oliveira Barateli
- Programa de Pós-graduação em Genética e Melhoramento de Plantas, Escola de Agronomia, Universidade Federal de Goiás, Goiânia, Goiás Brazil
- Laboratório de Genética e Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás Brazil
| | - Ueric José Borges de Souza
- Programa de Pós-graduação em Genética e Melhoramento de Plantas, Escola de Agronomia, Universidade Federal de Goiás, Goiânia, Goiás Brazil
- Laboratório de Genética e Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás Brazil
| | | | - Bianca Waléria Bertoni
- Unidade de Biotecnologia, Universidade de Ribeirão Preto, Ribeirão Preto, São Paulo Brazil
| | - Mariana Pires de Campos Telles
- Laboratório de Genética e Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás Brazil
- Escola de Ciências Agrárias e Biológicas, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás Brazil
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Bhandari MS, Meena RK, Shamoon A, Saroj S, Kant R, Pandey S. First de novo genome specific development, characterization and validation of simple sequence repeat (SSR) markers in Genus Salvadora. Mol Biol Rep 2020; 47:6997-7008. [PMID: 32930932 DOI: 10.1007/s11033-020-05758-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 08/28/2020] [Indexed: 11/29/2022]
Abstract
Salvadoraceae constitutes ecologically imperative desert families of 3 genera-Azima, Dobera and Salvadora. Under genus Salvadora of this family, S. oleoides is a keystone species of socio-economic and medicinal value. This species naturally grows in the arid zones but currently experiencing severe fragmentation due to land use change and reduced regeneration, which may have resulted in the depletion of genetic diversity. Hence, it is up-most important to develop genomic resources for studying the population genetics in S. oleoides. This study aims to develop robust microsatellites markers, which were not yet reported in genus Salvodora due to lack of genome sequence information. We developed novel microsatellites markers in S. oleoides using Illumina paired-end sequencing technology. In total, 14,552 simple sequence repeat (SSR) markers were successfully designed from 21,055 microsatellite repeats detected in the 13 Gb raw sequence data. Afterwards, a subset of 101 SSRs were randomly selected and validated, 94 primers were successfully amplified and 34 showed polymorphisms. These SSRs were used to estimate the measures of genetic diversity in three natural populations of state Rajasthan and Gujarat. Importantly, average number of alleles (Na), observed heterozygosity (Ho), expected heterozygosity (He), and polymorphism information content (PIC) were recorded as 2.4, 0.529, 0.357, and 0.326, respectively. Furthermore, 15 primers were evaluated in S. persica for cross-transferability, and all were successfully amplified but only eight showed polymorphisms. This study has been conducted first time for S. oleoides and pioneer among the native species of arid-zone in India.
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Affiliation(s)
- Maneesh S Bhandari
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand, 248 195, India.
| | - Rajendra K Meena
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand, 248 195, India
| | - Arzoo Shamoon
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand, 248 195, India
| | - Shanti Saroj
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand, 248 195, India
| | - Rama Kant
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, Uttarakhand, 248 195, India
| | - Shailesh Pandey
- Forest Pathology Discipline, Division of Forest Protection, Forest Research Institute, Dehradun, Uttarakhand, 248 006, India
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Yuan N, Li M, Jia C. De novo transcriptome assembly and population genetic analyses of an important coastal shrub, Apocynum venetum L. BMC PLANT BIOLOGY 2020; 20:408. [PMID: 32883231 PMCID: PMC7470449 DOI: 10.1186/s12870-020-02626-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 08/27/2020] [Indexed: 05/07/2023]
Abstract
BACKGROUND Apocynum venetum L. is an important medicinal plant that is mainly distributed in the coastal areas and northwest of China. In addition to its high medical and economic value, its adaptation to saline-alkali and coastal saline lands makes A. venetum an ideal candidate for use in vegetation restoration. To date, the study of A. venetum has been limited in the northwest region of China, little attention has been paid to the genetic diversity and population structure of A. venetum populations in the coastal region. Here, we performed transcriptome sequencing of total RNA from A. venetum leaves and developed efficient expressed sequence tag-simple sequence repeat (EST-SSR) markers for analyzing the genetic diversity and population structure of A. venetum in the coastal region. RESULTS A total of 86,890 unigenes were generated after de novo assembly, and 68,751 of which were successfully annotated by searching against seven protein databases. Furthermore, 14,072 EST-SSR loci were detected and 10,243 primer pairs were successfully designed from these loci. One hundred primer pairs were randomly selected and synthesized, twelve primer pairs were identified as highly polymorphic and further used for population genetic analysis. Population genetic analyses showed that A. venetum exhibited low level of genetic diversity (mean alleles per locus, NA = 3.3; mean expected heterozygosity, HE = 0.342) and moderate level of genetic differentiation among the populations (genetic differentiation index, FST = 0.032-0.220) in the coastal region. Although the contemporary (mean mc = 0.056) and historical (mean mh = 0.106) migration rates among the six A. venetum populations were moderate, a decreasing trend over the last few generations was detected. Bayesian structure analysis clustered six populations into two major groups, and genetic bottlenecks were found to have occurred in two populations (QG, BH). CONCLUSIONS Using novel EST-SSR markers, we evaluated the genetic variation of A. venetum in the coastal region and determined conservation priorities based on these findings. The large dataset of unigenes and SSRs identified in our study, combining samples from a broader range, will support further research on the conservation and evolution of this important coastal plant and its related species.
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Affiliation(s)
- Na Yuan
- Institute of Crop Germplasm and Biotechnology, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China.
| | - Mimi Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Chunlin Jia
- Institute of Agricultural and Sustainable Development, Shandong Academy of Agricultural Sciences, Jinan, China
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Verma P, Singh N, Khan SA, Mathur AK, Sharma A, Jamal F. TIAs pathway genes and associated miRNA identification in Vinca minor: supporting aspidosperma and eburnamine alkaloids linkage via transcriptomic analysis. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1695-1711. [PMID: 32801497 PMCID: PMC7415056 DOI: 10.1007/s12298-020-00842-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 06/16/2020] [Accepted: 06/22/2020] [Indexed: 05/17/2023]
Abstract
V. minor contains monomeric eburnamine-type of indole alkaloids having utilization as a neuro-medicinal plant. The biosynthetic pathway studies using miRNAs has been the focal point for plant genomic research in recent years and this technique is utilized to get an insight into a possible pathway level study in V. minor as understanding of genes in this prized medicinal plant is meagrely understood. The de novo transcriptomic analysis using Illumina Next gen sequencing has been performed in glasshouse shifted plant and transformed roots to elucidate the possible non confirmed steps of terpenoid indole alkaloids (TIAs) pathway in V. minor. A putative TIA pathway is elucidated in the study including twelve possible TIAs biosynthetic genes. The specific miRNA associated with TIAs pathway were identified and their roles were discussed for the first time in V. minor. The comparative analysis of transcriptomic data of glasshouse shifted plant and transformed roots showed that the raw reads of transformed roots were higher (83,740,316) compared to glasshouse shifted plant (67,733,538). The EST-SSR prediction showed the maximum common repeats among glasshouse shifted plant and transformed roots, although small variation was found in trinucleotide repeats restricted to glasshouse shifted plant. The study reveals overall 37 miRNAs which were observed to be true and can have a role in pathway as they can regulate the growth and alkaloid production. The identification of putative pathway genes plays an important role in establishing linkage between Aspidosperma and Eburnamine alkaloids.
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Affiliation(s)
- Priyanka Verma
- Department of Plant Biotechnology, CSIR-Central Institute of Medicinal and Aromatic Plants (CIMAP), PO-CIMAP, Lucknow, 226015 India
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory (NCL), Homi Bhabha Road, Pashan, Pune, 411008 India
| | - Noopur Singh
- Department of Plant Biotechnology, CSIR-Central Institute of Medicinal and Aromatic Plants (CIMAP), PO-CIMAP, Lucknow, 226015 India
| | - Shamshad Ahmad Khan
- Department of Plant Biotechnology, CSIR-Central Institute of Medicinal and Aromatic Plants (CIMAP), PO-CIMAP, Lucknow, 226015 India
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory (NCL), Homi Bhabha Road, Pashan, Pune, 411008 India
- Applied Biotechnology Department, Sur College of Applied Sciences, Ministry of Higher Education, Sur, 411 Oman
| | - Ajay Kumar Mathur
- Department of Plant Biotechnology, CSIR-Central Institute of Medicinal and Aromatic Plants (CIMAP), PO-CIMAP, Lucknow, 226015 India
| | - Ashok Sharma
- Department of Plant Biotechnology, CSIR-Central Institute of Medicinal and Aromatic Plants (CIMAP), PO-CIMAP, Lucknow, 226015 India
| | - Farrukh Jamal
- Biochemistry Division, Dr. R.M.L. Awadh University, Faizabad, 224001 India
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Zhou XJ, Liu MX, Lu XY, Sun SS, Cheng YW, Ya HY. Genome survey sequencing and identification of genomic SSR markers for Rhododendron micranthum. Biosci Rep 2020; 40:BSR20200988. [PMID: 32495827 PMCID: PMC7303352 DOI: 10.1042/bsr20200988] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/18/2020] [Accepted: 06/03/2020] [Indexed: 01/15/2023] Open
Abstract
Rhododendron micranthum is an evergreen shrub species widely distributed in China that has high ornamental and medicinal value. However, there is a lack of molecular and genomic data for this plant, which severely restricts the development of its relevant research. The objective of the present study was to conduct a first genomic survey of R. micranthum and determine its whole-genome sequencing scheme. Next-generation sequencing (Illumina Hi-Seq Xten) was used to measure the genome size of R. micranthum, K-mer analysis were employed to investigate its genomic profile. Finally, we conducted bioinformatics methods to performed SSR (simple sequence repeat) prediction based on the genomic data. The genome size of R. micranthum was estimated to be 554.22 Mb. The heterozygosity ratio was 0.93%, and the sequence repeat ratio was calculated to be 49.17%. The clean reads of R. micranthum were assembled into 2281551 scaffolds with a N50 value of 916 bp. A total of 479724 SSR molecular markers were identified in the R. micranthum genome, and 871656 pairs of primers designed for application. Among of them, 100 primer pairs were validated, and 71 primer pairs were successfully amplified. In summary, the R. micranthum genome is complex with high heterozygosity and low repeated sequences. In future whole-genome research in R. micranthum, higher-depth '2+3' (Illumina+PacBio) sequencing may yield better assembly results.
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Affiliation(s)
- Xiao-jun Zhou
- College of Life Science, Luoyang Normal University, 6 Jiqing Road, Luoyang 471934, China
| | - Meng-xue Liu
- College of Life Science, Luoyang Normal University, 6 Jiqing Road, Luoyang 471934, China
| | - Xiao-yu Lu
- College of Life Science, Luoyang Normal University, 6 Jiqing Road, Luoyang 471934, China
| | - Shan-shan Sun
- College of Life Science, Luoyang Normal University, 6 Jiqing Road, Luoyang 471934, China
| | - Yan-wei Cheng
- College of Life Science, Luoyang Normal University, 6 Jiqing Road, Luoyang 471934, China
| | - Hui-yuan Ya
- College of Life Science, Luoyang Normal University, 6 Jiqing Road, Luoyang 471934, China
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Fuchs EJ, Cascante-Marin A, Madrigal-Brenes R, Harvey N, Quesada M. Isolation and characterization of microsatellites for the neotropical dioecious palm Chamaedorea tepejilote (Arecaceae) and cross-amplification in other Chamaedorea species. Mol Biol Rep 2020; 47:6385-6391. [PMID: 32557191 DOI: 10.1007/s11033-020-05580-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/10/2020] [Indexed: 11/30/2022]
Abstract
Palms are important components of tropical and subtropical ecosystems and have even been considered keystone plant resources that can support a large array of pollinators and frugivores. Palms are also economically important. Chamaedorea tepejilote Liebm. is a widely distributed palm with important bioeconomic potential for food, traditional medicine and ornamental purposes. Eighteen microsatellite primers were developed for C. tepejilote. Polymorphism and genetic diversity were evaluated in 71 individuals from four populations in Costa Rica. Thirteen loci were polymorphic and the number of alleles in the pooled sample ranged between 5 and 20, the average number of alleles was 10.61. Average observed heterozygosity was Ho = 0.607 ± 0.04 (SD) and the average expected heterozygosity was He = 0.600 ± 0.03. The exclusion probability of the combined 13 loci, was PE = 0.998. We tested transferability of the markers in the congeneric C. costaricana, C. pinnantifrons and C. macrospadix. Dioecious species are common in tropical forests; however, few studies have analyzed gene flow patterns in these species. The markers developed for C. tepejilote are an important tool to quantify gene flow patterns and the distribution of genetic diversity within populations. This information will be useful for the development of conservation and management practices of this dioecious tropical palm species.
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Affiliation(s)
- Eric J Fuchs
- Escuela de Biología, Universidad de Costa Rica, San José, 11501-2060, Costa Rica
- Laboratorio Nacional de Análisis y Síntesis Ecológica (LANASE), Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Morelia, Michoacán, Mexico
| | | | - Ruth Madrigal-Brenes
- Escuela de Biología, Universidad de Costa Rica, San José, 11501-2060, Costa Rica
| | | | - Mauricio Quesada
- Laboratorio Nacional de Análisis y Síntesis Ecológica (LANASE), Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Morelia, Michoacán, Mexico.
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Morelia, Michoacán, Mexico.
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Liu Q, Lu Z, He W, Li F, Chen W, Li C, Chao Z, Tian E. Development and characterization of 16 novel microsatellite markers by Transcriptome sequencing for Angelica dahurica and test for cross-species amplification. BMC PLANT BIOLOGY 2020; 20:152. [PMID: 32268882 PMCID: PMC7140362 DOI: 10.1186/s12870-020-02374-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/31/2020] [Indexed: 05/31/2023]
Abstract
BACKGROUND Angelica dahurica (Apiaceae) is an important herb in traditional Chinese medicine. Because of its important medicinal and economic values, its wild resources were over-exploited and increasingly reduced. Meanwhile, the diversity of cultivars of A. dahurica has decreased as a result of long-term artificial cultivation. However, there are no population genetics studies of natural A. dahurica reported yet, especially for using microsatellite markers (SSRs) to investigate population genetics of the species. RESULTS Sixteen polymorphic EST-SSR loci were isolated from A. dahurica with transcriptome sequencing technology (RNA-Seq). The number of alleles varied from 2 to 15 per polymorphic locus over populations with the observed and expected heterozygosities ranging from 0.000 to 1.000 and from 0.000 to 0.829, respectively. Significant deviations from Hardy-Weinberg equilibrium were observed at 8 loci. Tests of linkage disequilibrium showed 11 informative locus pairs were significant across all populations. Cross-species amplification showed that 14 out of 16 SSR loci have the transferability in cultivar-A. dahurica cv. 'Hangbaizhi' and A. decursiva. CONCLUSIONS The 16 newly developed loci microsatellite primers with RNA-Seq will be useful for further investigating population genetics of A. dahurica, cultivars and other members of this genus.
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Affiliation(s)
- Qianqian Liu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, 510095, China
| | - Zuyu Lu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 515005, China
| | - Wei He
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 515005, China
| | - Fang Li
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 515005, China
| | - Wenna Chen
- College of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, 056038, China
| | - Chan Li
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 515005, China
| | - Zhi Chao
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 515005, China.
| | - Enwei Tian
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 515005, China.
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Zhang Y, Ge M, Wang X, Zeng Y, Liao Y, Wang Y, Zeng Z. Discrimination of Moutan Cortex from different sources and geographical origins for quality evaluation using microsatellite markers coupled with chemical analysis. BIOCHEM SYST ECOL 2020. [DOI: 10.1016/j.bse.2020.104005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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