1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Graham RE, Reyes-Betancort JA, Chapman MA, Carine MA. Inter-island differentiation and contrasting patterns of diversity in the iconic Canary Island sub-alpine endemic Echium wildpretii (Boraginaceae). SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1877847] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Rachael E. Graham
- Algae, Fungi and Plants Division, Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
- Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - J. Alfredo Reyes-Betancort
- Jardín de Aclimatación de La Orotava, Instituto Canario de Investigaciones Agrarias (ICIA), C/Retama 2, Puerto de la Cruz, 38400, Tenerife, Spain
| | - Mark A. Chapman
- Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Mark A. Carine
- Algae, Fungi and Plants Division, Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| |
Collapse
|
3
|
White OW, Reyes-Betancort JA, Chapman MA, Carine MA. Geographical isolation, habitat shifts and hybridisation in the diversification of the Macaronesian endemic genus Argyranthemum (Asteraceae). THE NEW PHYTOLOGIST 2020; 228:1953-1971. [PMID: 33006142 DOI: 10.1111/nph.16980] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 09/16/2020] [Indexed: 06/11/2023]
Abstract
Inferring the processes responsible for the rich endemic diversity of oceanic island floras is important for our understanding of plant evolution and setting practical conservation priorities. This requires an accurate knowledge of phylogenetic relationships, which have often been difficult to resolve due to a lack of genetic variation. We employed genotyping-by-sequencing (GBS) to investigate how geographical isolation, habitat shifts, and hybridisation have contributed to the evolution of diversity observed in Argyranthemum Webb (Asteraceae), the largest genus of flowering plants endemic to the Macaronesian archipelagos. Species relationships were resolved, and biogeographical stochastic mapping identified intra-island speciation as the most frequent biogeographic process underlying diversification, contrary to the prevailing view in Argyranthemum and the Canary Islands. D-statistics revealed significant evidence of hybridisation between lineages co-occurring on the same island, however there was little support for the hypothesis that hybridisation may be responsible for the occurrence of nonmonophyletic multi-island endemic (MIE) species. Geographic isolation, habitat shifts and hybridisation have all contributed to the diversification of Argyranthemum, with intra-island speciation found to be more frequent than previously thought. Morphological convergence is also proposed to explain the occurrence of nonmonophyletic MIE species. This study reveals greater complexity in the evolutionary processes generating Macaronesian endemic diversity.
Collapse
Affiliation(s)
- Oliver W White
- Algae, Fungi and Plants Division, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
- Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UK
| | - J Alfredo Reyes-Betancort
- Jardín de Aclimatación de La Oratava, Instituto Canario de Investigaciones Agrarias - ICIA), C/ Retama 2, Puerto de la Cruz, Tenerife, 38400, Spain
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Mark A Carine
- Algae, Fungi and Plants Division, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| |
Collapse
|
4
|
Karcι H, Paizila A, Topçu H, Ilikçioğlu E, Kafkas S. Transcriptome Sequencing and Development of Novel Genic SSR Markers From Pistacia vera L. Front Genet 2020; 11:1021. [PMID: 33033493 PMCID: PMC7509152 DOI: 10.3389/fgene.2020.01021] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/10/2020] [Indexed: 01/28/2023] Open
Abstract
In this study, we aimed to develop novel genic simple sequence repeat (eSSR) markers and to study phylogenetic relationship among Pistacia species. Transcriptome sequencing was performed in different tissues of Siirt and Atl cultivars of pistachio (Pistacia vera). A total of 37.5-Gb data were used in the assembly. The number of total contigs and unigenes was calculated as 98,831, and the length of N50 was 1,333 bp after assembly. A total of 14,308 dinucleotide, trinucleotide, tetranucleotide, pentanucleotide, and hexanucleotide SSR motifs (4–17) were detected, and the most abundant SSR repeat types were trinucleotide (29.54%), dinucleotide (24.06%), hexanucleotide (20.67%), pentanucleotide (18.88%), and tetranucleotide (6.85%), respectively. Overall 250 primer pairs were designed randomly and tested in eight Pistacia species for amplification. Of them, 233 were generated polymerase chain reaction products in at least one of the Pistacia species. A total of 55 primer pairs that had amplifications in all tested Pistacia species were used to characterize 11 P. vera cultivars and 78 wild Pistacia genotypes belonging to nine Pistacia species (P. khinjuk, P. eurycarpa, P. atlantica, P. mutica, P. integerrima, P. chinensis, P. terebinthus, P. palaestina, and P. lentiscus). A total of 434 alleles were generated from 55 polymorphic eSSR loci with an average of 7.89 alleles per locus. The mean number of effective allele was 3.40 per locus. Polymorphism information content was 0.61, whereas observed (Ho) and expected heterozygosity (He) values were 0.39 and 0.65, respectively. UPGMA (unweighted pair-group method with arithmetic averages) and STRUCTURE analysis divided 89 Pistacia genotypes into seven populations. The closest species to P. vera was P. khinjuk. P. eurycarpa was closer P. atlantica than P. khinjuk. P. atlantica–P. mutica and P. terebinthus–P. palaestina pairs of species were not clearly separated from each other, and they were suggested as the same species. The present study demonstrated that eSSR markers can be used in the characterization and phylogenetic analysis of Pistacia species and cultivars, as well as genetic linkage mapping and QTL (quantitative trait locus) analysis.
Collapse
Affiliation(s)
- Harun Karcι
- Department of Horticulture, Faculty of Agriculture, Çukurova University, Adana, Turkey
| | - Aibibula Paizila
- Department of Horticulture, Faculty of Agriculture, Çukurova University, Adana, Turkey
| | - Hayat Topçu
- Department of Horticulture, Faculty of Agriculture, Çukurova University, Adana, Turkey
| | | | - Salih Kafkas
- Department of Horticulture, Faculty of Agriculture, Çukurova University, Adana, Turkey
| |
Collapse
|
5
|
Chai M, Ye H, Wang Z, Zhou Y, Wu J, Gao Y, Han W, Zang E, Zhang H, Ru W, Sun G, Wang Y. Genetic Divergence and Relationship Among Opisthopappus Species Identified by Development of EST-SSR Markers. Front Genet 2020; 11:177. [PMID: 32194635 PMCID: PMC7065708 DOI: 10.3389/fgene.2020.00177] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/13/2020] [Indexed: 12/16/2022] Open
Abstract
Opisthopappus Shih is an endemic and endangered genus restricted to the Taihang Mountains that has important ornamental and economic value. According to the Flora Reipublicae Popularis Sinicae (FRPS, Chinese version), this genus contains two species (Opisthopappus longilobus and Opisthopappus taihangensis), whereas in the Flora of China (English version) only one species O. taihangensis is present. The interspecific phylogenetic relationship remains unclear and undefined, which might primarily be due to the lack of specific molecular markers for phylogenetic analysis. For this study, 2644 expressed sequence tag-simple sequence repeats (EST-SSRs) from 33,974 unigenes using a de novo transcript assembly of Opisthopappus were identified with a distribution frequency of 7.78% total unigenes. Thereinto, mononucleotides (1200, 45.39%) were the dominant repeat motif, followed by trinucleotides (992, 37.52%), and dinucleotides (410, 15.51%). The most dominant trinucleotide repeat motif was ACC/GGT (207, 20.87%). Based on the identified EST-SSRs, 245 among 1444 designed EST-SSR primers were selected for the development of potential molecular markers. Among these markers, 63 pairs of primers (25.71%) generated clear and reproducible bands with expected sizes. Eventually, 11 primer pairs successfully amplified all individuals from the studied populations. Through the EST-SSR markers, a high level of genetic diversity was detected between Opisthopappus populations. A significant genetic differentiation between the O. longilobus and O. taihangensis populations was found. All studied populations were divided into two clusters by UPGMA, NJ, STRUCTURE, and PCoA. These results fully supported the view of the FRPS, namely, that O. longilobus and O. taihangensis should be regarded as two distinct species. Our study demonstrated that transcriptome sequences, as a valuable tool for the quick and cost-effective development of molecular markers, was helpful toward obtaining comprehensive EST-SSR markers that could contribute to an in-depth assessment of the genetic and phylogenetic relationships between Opisthopappus species.
Collapse
Affiliation(s)
- Min Chai
- School of Life Sciences, Shanxi Normal University, Linfen, China
| | - Hang Ye
- School of Life Sciences, Shanxi Normal University, Linfen, China
| | - Zhi Wang
- School of Life Sciences, Shanxi Normal University, Linfen, China
| | - Yuancheng Zhou
- Triticeae Research Institute, Shanxi Academy of Agricultural Science, Linfen, China
| | - Jiahui Wu
- School of Life Sciences, Shanxi Normal University, Linfen, China.,Changzhi University, Changzhi, China
| | - Yue Gao
- School of Life Sciences, Shanxi Normal University, Linfen, China
| | - Wei Han
- School of Life Sciences, Shanxi Normal University, Linfen, China
| | - En Zang
- School of Life Sciences, Shanxi Normal University, Linfen, China
| | - Hao Zhang
- School of Life Sciences, Shanxi Normal University, Linfen, China
| | | | - Genlou Sun
- Department of Biology, Saint Mary's University, Halifax, NS, Canada
| | - Yling Wang
- School of Life Sciences, Shanxi Normal University, Linfen, China
| |
Collapse
|
6
|
Taheri S, Abdullah TL, Rafii MY, Harikrishna JA, Werbrouck SPO, Teo CH, Sahebi M, Azizi P. De novo assembly of transcriptomes, mining, and development of novel EST-SSR markers in Curcuma alismatifolia (Zingiberaceae family) through Illumina sequencing. Sci Rep 2019; 9:3047. [PMID: 30816255 PMCID: PMC6395698 DOI: 10.1038/s41598-019-39944-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 02/06/2019] [Indexed: 11/24/2022] Open
Abstract
Curcuma alismatifolia widely used as an ornamental plant in Thailand and Cambodia. This species of herbaceous perennial from the Zingiberaceae family, includes cultivars with a wide range of colours and long postharvest life, and is used as an ornamental cut flower, as a potted plant, and in exterior landscapes. For further genetic improvement, however, little genomic information and no specific molecular markers are available. The present study used Illumina sequencing and de novo transcriptome assembly of two C. alismatifolia cvs, 'Chiang Mai Pink' and 'UB Snow 701', to develop simple sequence repeat markers for genetic diversity studies. After de novo assembly, 62,105 unigenes were generated and 48,813 (78.60%) showed significant similarities versus six functional protein databases. In addition, 9,351 expressed sequence tag-simple sequence repeats (EST-SSRs) were identified with a distribution frequency of 12.5% total unigenes. Out of 8,955 designed EST-SSR primers, 150 primers were selected for the development of potential molecular markers. Among these markers, 17 EST-SSR markers presented a moderate level of genetic diversity among three C. alismatifolia cultivars, one hybrid, three Curcuma, and two Zingiber species. Three different genetic groups within these species were revealed using EST-SSR markers, indicating that the markers developed in this study can be effectively applied to the population genetic analysis of Curcuma and Zingiber species. This report describes the first analysis of transcriptome data of an important ornamental ginger cultivars, also provides a valuable resource for gene discovery and marker development in the genus Curcuma.
Collapse
Affiliation(s)
- Sima Taheri
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
- Centre of Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Thohirah Lee Abdullah
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - M Y Rafii
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Jennifer Ann Harikrishna
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
- Centre of Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Stefaan P O Werbrouck
- Laboratory of Applied Science In Vitro Plant Biotechnology, Department of Plants and Crops, Faculty of Bioscience Engineering, University Ghent, Valentin Vaerwyckweg 1, BE-9000, Gent, Belgium
| | - Chee How Teo
- Centre of Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Mahbod Sahebi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Parisa Azizi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| |
Collapse
|
7
|
White OW, Reyes-Betancort A, Chapman MA, Carine MA. Independent homoploid hybrid speciation events in the Macaronesian endemic genus Argyranthemum. Mol Ecol 2018; 27:4856-4874. [DOI: 10.1111/mec.14889] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 08/29/2018] [Accepted: 09/26/2018] [Indexed: 01/03/2023]
Affiliation(s)
- Oliver W. White
- Algae, Fungi and Plants Division; Department of Life Sciences; The Natural History Museum; London UK
- Biological Sciences; University of Southampton; Southampton UK
| | | | - Mark A. Chapman
- Biological Sciences; University of Southampton; Southampton UK
| | - Mark A. Carine
- Algae, Fungi and Plants Division; Department of Life Sciences; The Natural History Museum; London UK
| |
Collapse
|
8
|
Rodríguez-Rodríguez P, Fernández de Castro AG, Sosa PA. The restoration of the endangered Sambucus palmensis after 30 years of conservation actions in the Garajonay National Park: genetic assessment and niche modeling. PeerJ 2018; 6:e4985. [PMID: 29910987 PMCID: PMC6003393 DOI: 10.7717/peerj.4985] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 05/25/2018] [Indexed: 11/20/2022] Open
Abstract
The translocation of individuals or the reinforcement of populations are measures in the genetic rescue of endangered species. Although it can be controversial to decide which and how many individuals must be reintroduced, populations can benefit from reinforcements. Sambucus palmensis is a critically endangered endemic to the Canary Islands. During the past 30 years, the Garajonay National Park (La Gomera) has carried out an intensive program of translocations using cuttings, due to the low germination rates of seeds. To assess the effect of the restorations on the population genetics of S. palmensis in La Gomera, we collected 402 samples from all the restored sites and all known natural individuals, which were genotyped with seven microsatellite markers. In addition, we conducted a species distribution modeling approach to assess how restorations fit the ecological niche of the species. Results show that there is a high proportion of clone specimens due to the propagation method, and the natural clonal reproduction of the species. Nonetheless, the observed heterozygosity has increased with the restorations and there still are private alleles and unique genotypes in the natural populations that have not been considered in the restorations. The population of Liria constitutes a very important genetic reservoir for the species. To optimize future reintroductions, we have proposed a list of specimens that are suitable for the extraction of seeds or cuttings in a greenhouse, as well as new suitable areas obtained by the species distribution models.
Collapse
Affiliation(s)
- Priscila Rodríguez-Rodríguez
- Instituto Universitario de Estudios Ambientales y Recursos Naturales (IUNAT), Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Canary Islands, Spain
| | | | - Pedro A Sosa
- Instituto Universitario de Estudios Ambientales y Recursos Naturales (IUNAT), Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Canary Islands, Spain
| |
Collapse
|
9
|
Taheri S, Lee Abdullah T, Yusop MR, Hanafi MM, Sahebi M, Azizi P, Shamshiri RR. Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants. Molecules 2018; 23:E399. [PMID: 29438290 PMCID: PMC6017569 DOI: 10.3390/molecules23020399] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 01/11/2018] [Accepted: 01/13/2018] [Indexed: 11/17/2022] Open
Abstract
Microsatellites, or simple sequence repeats (SSRs), are one of the most informative and multi-purpose genetic markers exploited in plant functional genomics. However, the discovery of SSRs and development using traditional methods are laborious, time-consuming, and costly. Recently, the availability of high-throughput sequencing technologies has enabled researchers to identify a substantial number of microsatellites at less cost and effort than traditional approaches. Illumina is a noteworthy transcriptome sequencing technology that is currently used in SSR marker development. Although 454 pyrosequencing datasets can be used for SSR development, this type of sequencing is no longer supported. This review aims to present an overview of the next generation sequencing, with a focus on the efficient use of de novo transcriptome sequencing (RNA-Seq) and related tools for mining and development of microsatellites in plants.
Collapse
Affiliation(s)
- Sima Taheri
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Thohirah Lee Abdullah
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mohd Rafii Yusop
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mohamed Musa Hanafi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
- Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mahbod Sahebi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Parisa Azizi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Redmond Ramin Shamshiri
- Smart Farming Technology Research Center, Department of Biological and Agricultural Engineering, Faculty of Engineering, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| |
Collapse
|
10
|
Sreedhar RV, Prasad P, Reddy LPA, Rajasekharan R, Srinivasan M. Unravelling a stearidonic acid-rich triacylglycerol biosynthetic pathway in the developing seeds of Buglossoides arvensis: A transcriptomic landscape. Sci Rep 2017; 7:10473. [PMID: 28874672 PMCID: PMC5585386 DOI: 10.1038/s41598-017-09882-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 07/31/2017] [Indexed: 01/07/2023] Open
Abstract
Buglossoides arvensis is an emerging oilseed crop that is rich in stearidonic acid (SDA) and has several potential applications in human health and nutrition. The molecular basis of SDA biosynthesis in this plant remains unknown due to lack of genomic information. To unravel key genes involved in SDA-rich triacylglycerol (TAG) biosynthesis, we performed transcriptome sequencing of pooled mRNA from five different developmental stages of B. arvensis seeds using Illumina NextSeq platform. De novo transcriptome assembly generated 102,888 clustered transcripts from 39.83 million high-quality reads. Of these, 62.1% and 55.54% of transcripts were functionally annotated using Uniprot-Viridiplantae and KOG databases, respectively. A total of 10,021 SSR-containing sequences were identified using the MISA tool. Deep mining of transcriptome assembly using in silico tools led to the identification of genes involved in fatty acid and TAG biosynthesis. Expression profiling of 17 key transcripts involved in fatty acid desaturation and TAG biosynthesis showed expression patterns specific to the development stage that positively correlated with polyunsaturated fatty acid accumulation in the developing seeds. This first comprehensive transcriptome analysis provides the basis for future research on understanding molecular mechanisms of SDA-rich TAG accumulation in B. arvensis and aids in biotechnological production of SDA in other oilseed crops.
Collapse
Affiliation(s)
- R V Sreedhar
- Department of Lipid Science, CSIR-Central Food Technological Research Institute (CSIR-CFTRI), Mysuru, 570020, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-Central Food Technological Research Institute Campus, Mysuru, 570020, India
| | - P Prasad
- Department of Lipid Science, CSIR-Central Food Technological Research Institute (CSIR-CFTRI), Mysuru, 570020, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-Central Food Technological Research Institute Campus, Mysuru, 570020, India
| | - L Prasanna Anjaneya Reddy
- Department of Lipid Science, CSIR-Central Food Technological Research Institute (CSIR-CFTRI), Mysuru, 570020, India
| | - Ram Rajasekharan
- Department of Lipid Science, CSIR-Central Food Technological Research Institute (CSIR-CFTRI), Mysuru, 570020, India
| | - Malathi Srinivasan
- Department of Lipid Science, CSIR-Central Food Technological Research Institute (CSIR-CFTRI), Mysuru, 570020, India.
| |
Collapse
|
11
|
Cohen JI. De novo Sequencing and Comparative Transcriptomics of Floral Development of the Distylous Species Lithospermum multiflorum. FRONTIERS IN PLANT SCIENCE 2016; 7:1934. [PMID: 28066486 PMCID: PMC5179544 DOI: 10.3389/fpls.2016.01934] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 12/06/2016] [Indexed: 06/06/2023]
Abstract
Genes controlling the morphological, micromorphological, and physiological components of the breeding system distyly have been hypothesized, but many of the genes have not been investigated throughout development of the two floral morphs. To this end, the present study is an examination of comparative transcriptomes from three stages of development for the floral organs of the morphs of Lithospermum multiflorum. Transcriptomes of flowers of the two morphs, from various stages of development, were sequenced using an Illumina HiSeq 2000. The floral transcriptome of L. multiflorum was assembled, and differential gene expression (DE) was identified between morphs, throughout development. Additionally, Gene Ontology (GO) terms for DE genes were determined. Fewer genes were DE early in development compared to later in development, with more genes highly expressed in the gynoecium of the SS morph and the corolla and androecium of the LS morph. A reciprocal pattern was observed later in development, and many more genes were DE during this latter stage. During early development, DE genes appear to be involved in growth and floral development, and during later development, DE genes seem to affect physiological functions. Interestingly, many genes involved in response to stress were identified as DE between morphs.
Collapse
|