Generation and Characterisation of a Reference Transcriptome for Lentil (Lens culinaris Medik.)

Sudheesh, Shimna; Verma, Preeti; Forster, John W.; Cogan, Noel O. I.; Kaur, Sukhjiwan

doi:10.3390/ijms17111887

Cited by 49 publications

(53 citation statements)

References 62 publications

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“…The final Doza assembly resulted in 58,962 transcripts with total assembly length of 66,959,534 bp (average length 1135.6 bp and N50 of 1595), whereas the final Farah assembly comprised of 53,275 transcripts with total assembly length of 60,943,125 bp (average length 1143.9 bp and N50 of 1683). Both the Doza and Farah assemblies contained a substantial number of large transcripts with sequence length >500 bp (average 67.3%), which was comparable to the results obtained by previous studies [40,50] with a deep sequencing method for transcriptome generation. These results are highly comparable to those for the transcriptomes of other legume species, such as M. truncatula, which has a total of 66,028,174 bp (M. truncatula Genome Project v. 4.0), and soybean, which has 68,278,578 bp [51], and much higher than that of chickpea, which has 32,973,966 bp [52].…”

Section: De Novo Transcriptome Assemblysupporting

confidence: 75%

“…Based on the number of unigenes, it can be concluded that the Farah assembly is less fragmented (23.6%) than the Doza assembly (37.9%). The number of unigenes obtained from this study is highly comparable to those from other legume genomes including chickpea (28,269 gene models [52]) and lentil (27,396 unigenes based on the Nr database [50]). Moreover, BLASTX analysis revealed that the largest number of matches were to M. truncatula (around 43% and 34% for Doza and Farah, respectively), followed by chickpea (approximately 22% for Doza and 16% for Farah), and then any other plant species.…”

Section: Annotation Of the Transcriptome Assembliessupporting

confidence: 54%

“…GO analysis revealed a total of 51.2% transcripts from Doza and 50.1% from Farah were assigned at least one GO term which is comparable with other similar studies published in the literature [23,50]. The unannotated sequences (approximately 20.1%) were evaluated for the presence of ORFs and further for the similarity searches in the alternate cultivar that had annotations and the presence of ORF.…”

Section: Annotation Of the Transcriptome Assembliesmentioning

confidence: 54%

“…The unannotated sequences (approximately 20.1%) were evaluated for the presence of ORFs and further for the similarity searches in the alternate cultivar that had annotations and the presence of ORF. The genes that were not annotated were more likely to be cultivar-specific and were included in the final assemblies for the completeness of the study as a previous study by Sudheesh et al [50] also reported a similar percentage (21%) of unannotated genome components in their transcriptome study.…”

Section: Annotation Of the Transcriptome Assembliesmentioning

confidence: 57%

“…RNA-Seq libraries from multiple tissue sources were sequenced to obtain differential tissue gene expression levels based on the approach previously used in field pea and lentil [45,50]. Significant proportions of transcripts (96.3% in Doza and 96.7% in Farah) were expressed in more than one source tissue, but showed varying expression levels.…”

Section: Analysis and Validation Of Tissue-specific Gene Expression Lmentioning

confidence: 99%

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Characterisation of Faba Bean (Vicia faba L.) Transcriptome Using RNA-Seq: Sequencing, De Novo Assembly, Annotation, and Expression Analysis

et al. 2017

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RNA sequencing (RNA-Seq) is a deep sequencing method used for transcriptome profiling. RNA-Seq assemblies have successfully been used for a broad variety of applications, such as gene characterisation, functional genomic studies, and gene expression analysis, particularly useful in the absence of a well-studied genome reference sequence. This study reports on the development of reference unigene sets from faba bean using RNA-Seq. Two Australian faba bean cultivars (Doza and Farah) that differ in terms of disease resistance, breeding habit, and adaptation characteristics, and have been extensively used in breeding programs, were utilised in this study. The de novo assembly resulted in a total of 58,962 and 53,275 transcripts with approximately 67 Mbp (1588 bp N50) and 61 Mbp (1629 bp N50) for Doza and Farah, respectively. The generated transcripts have been compared to the protein and nucleotide databases of NCBI, as well as to the gene complements of several related legume species such as Medicago truncatula, soybean, and chickpea. Both assemblies were compared to previously-published faba bean transcriptome reference sets for the degree of completeness and utility. Annotation of unigenes has been performed, and patterns of tissue-specific expression identified. The gene complement derived from this comprehensive transcriptome analysis shows that faba bean, despite its complex 13 Gbp genome, compares well to other legumes in expressed gene content. This study in faba bean represents the most comprehensive reference transcriptomes from two different Australian cultivars available to date and it provides a valuable resource for future genomics-assisted breeding activities in this species.

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Section: De Novo Transcriptome Assemblysupporting

confidence: 75%

Section: Annotation Of the Transcriptome Assembliessupporting

confidence: 54%

Section: Annotation Of the Transcriptome Assembliesmentioning

confidence: 54%

Section: Annotation Of the Transcriptome Assembliesmentioning

confidence: 57%

Section: Analysis and Validation Of Tissue-specific Gene Expression Lmentioning

confidence: 99%

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Characterisation of Faba Bean (Vicia faba L.) Transcriptome Using RNA-Seq: Sequencing, De Novo Assembly, Annotation, and Expression Analysis

et al. 2017

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Capturing variation in Lens (Fabaceae): Development and utility of an exome capture array for lentil

et al. 2018

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Premise of the StudyLentil is an important legume crop with reduced genetic diversity caused by domestication bottlenecks. Due to its large and complex genome, tools for reduced representation sequencing are needed. We developed an exome capture array for use in various genetic diversity studies.MethodsBased on the CDC Redberry draft genome, we developed an exome capture array using multiple sources of transcript resources. The probes were designed to target not only the cultivated lentil, but also wild species. We assessed the utility of the developed method by applying the generated data set to population structure and phylogenetic analyses.ResultsThe data set includes 16 wild lentils and 22 cultivar accessions of lentil. Alignment rates were over 90%, and the genic regions were well represented in the capture array. After stringent filtering, 6.5 million high‐quality variants were called, and the data set was used to assess the interspecific relationships within the genus Lens.DiscussionThe developed exome capture array provides large amounts of genomic data to be used in many downstream analyses. The method will have useful applications in marker‐assisted breeding programs aiming to improve the quality of cultivated lentil.

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Intelligent Characterization of Lentil Genetic Resources: Evolutionary History, Genetic Diversity of Germplasm, and the Need for Well‐Represented Collections

et al. 2021

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The genetic and phenotypic characterization of crops allows us to elucidate their evolutionary and domestication history, the genetic basis of important traits, and the use of variation present in landraces and wild relatives to enhance resilience. In this context, we aim to provide an overview of the main genetic resources developed for lentil and their main outcomes, and to suggest protocols for continued work on this important crop. Lens culinaris is the third-mostimportant cool-season grain and its use is increasing as a quick-cooking, nutritious, plant-based source of protein. L. culinaris was domesticated in the Fertile Crescent, and six additional wild taxa (L. orientalis, L. tomentosus, L. odemensis, L. lamottei, L. ervoides, and L. nigricans) are recognized. Numerous genetic diversity studies have shown that wild relatives present high levels of genetic variation and provide a reservoir of alleles that can be used for breeding programs. Furthermore, the integration of genetics/genomics and breeding techniques has resulted in identification of quantitative trait loci and genes related to attributes of interest. Genetic maps, massive genotyping, marker-assisted selection, and genomic selection are some of the genetic resources generated and applied in lentil. In addition, despite its size (∼4 Gbp) and complexity, the L. culinaris genome has been assembled, allowing a deeper understanding of its architecture. Still, major knowledge gaps exist in lentil, and a deeper understanding and characterization of germplasm resources, including wild relatives, is critical to lentil breeding and improvement.

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Generation and Characterisation of a Reference Transcriptome for Lentil (Lens culinaris Medik.)

Cited by 49 publications

References 62 publications

Characterisation of Faba Bean (Vicia faba L.) Transcriptome Using RNA-Seq: Sequencing, De Novo Assembly, Annotation, and Expression Analysis

Characterisation of Faba Bean (Vicia faba L.) Transcriptome Using RNA-Seq: Sequencing, De Novo Assembly, Annotation, and Expression Analysis

Capturing variation in Lens (Fabaceae): Development and utility of an exome capture array for lentil

Intelligent Characterization of Lentil Genetic Resources: Evolutionary History, Genetic Diversity of Germplasm, and the Need for Well‐Represented Collections

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