Transcriptome profiling of the floral buds and discovery of genes related to sex-differentiation in the dioecious cucurbit Coccinia grandis (L.) Voigt

Mohanty, Jatindra Nath; Nayak, Sanghamitra; Jha, Sumita; Joshi, Raj Kumar

doi:10.1016/j.gene.2017.05.058

Cited by 22 publications

(15 citation statements)

References 67 publications

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“…The clean reads were assembled de novo by using the Trinity package with default parameters, which has been used successfully for many nonreference species because of its outstanding performance for data from various settings [ 14 – 16 ]. Furthermore, the CD-HIT package was applied with default parameters to reduce redundancy from transcripts derived from homologous genes or from different alleles of the same gene, resulting in final assembly of a full-length transcript according to the de Bruijn graph theory, which uses variable transcript splicing characteristics [ 17 ].…”

Section: Methodsmentioning

confidence: 99%

De Novo assembly, characterization and development of EST-SSRs from Bletilla striata transcriptomes profiled throughout the whole growing period

Chen

Aci

et al. 2018

PLoS ONE

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Bletilla striata is an endangered orchid that has been used for millennia as a medicinal herb, in cosmetics and as a horticultural plant. To construct the first nucleotide database for this species and to develop abundant EST-SSR markers for facilitating further studies, various tissues and organs of plants in the main developmental stages were harvested for mRNA isolation and subsequent RNA sequencing. A total of 106,054,784 clean reads were generated by using Illumina paired-end sequencing technology. The reads were assembled into 127,261 unigenes by the Trinity package; the unigenes had an average length of 612 bp and an N50 of 957 bp. Of these unigenes, 67,494 (51.86%) were annotated in a series of databases. Of these annotated unigenes, 41,818 and 24,615 were assigned to gene ontology categories and clusters of orthologous groups, respectively. Additionally, 20,764 (15.96%) unigenes were mapped onto 275 pathways using the KEGG database. In addition, 25,935 high-quality EST-SSR primer pairs were developed from the 15,433 unigenes by MISA mining. To validate the accuracy of the newly designed markers, 87 of 100 randomly selected primers were effectively amplified; 63 of those yielded PCR products of the expected size, and 25 yielded products with significant amounts of polymorphism among the 4 landraces. Furthermore, the transferability test of the 25 polymorphic markers was performed in 6 individuals of two closely related genus Phalaenopsis and dendrobium. Which results showed a total of 5 markers can successfully amplified among these populations. This research provides a comprehensive nucleotide database and lays a solid foundation for functional gene mining and genomic research in B. striata. The developed EST-SSR primers could facilitate phylogenetic studies and breeding.

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Section: Methodsmentioning

confidence: 99%

De Novo assembly, characterization and development of EST-SSRs from Bletilla striata transcriptomes profiled throughout the whole growing period

Chen

Aci

et al. 2018

PLoS ONE

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“…Expansion and shrinkage are parallel processes in shaping the Y chromosome structure, varying in the impact on Y chromosome dynamics in individual stages of sex chromosome evolution [ 2 ] ( Table 1 ). Although a number of important studies on sex determination and sex chromosome evolution have emerged recently [ 3 , 4 , 5 ], we focus mainly on the impact of repetitive DNA on Y chromosome dynamics in advanced stages of sex chromosome divergence. Since there is a lack of information in plant models possessing ZZ/ZW [ 6 , 7 ], we review mainly XX/XY chromosomal systems with heteromorphic and/or heterochromatin-containing sex chromosomes.…”

Section: Introductionmentioning

confidence: 99%

Impact of Repetitive Elements on the Y Chromosome Formation in Plants

Hobza

Čegan

Jesionek

et al. 2017

Genes

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In contrast to animals, separate sexes and sex chromosomes in plants are very rare. Although the evolution of sex chromosomes has been the subject of numerous studies, the impact of repetitive sequences on sex chromosome architecture is not fully understood. New genomic approaches shed light on the role of satellites and transposable elements in the process of Y chromosome evolution. We discuss the impact of repetitive sequences on the structure and dynamics of sex chromosomes with specific focus on Rumex acetosa and Silene latifolia. Recent papers showed that both the expansion and shrinkage of the Y chromosome is influenced by sex-specific regulation of repetitive DNA spread. We present a view that the dynamics of Y chromosome formation is an interplay of genetic and epigenetic processes.

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“…Southern hybridization was performed as described previously (Mohanty et al 2017). Briefly, the genomic DNA (10 µg) isolated from M. dioica was digested with restriction endonucleases EcoRI, XbaI and HindIII.…”

Section: Southern Blot Analysismentioning

confidence: 99%

“…In the gourd family (Cucurbitaceae), flowers are represented by all the three major sexual patternsmonoecy, dioecy and hermaphrodite representing a distinct sexual dimorphism and evolution among the angiosperms. Although, major Cucurbitaceous genus such as Bryonia, Coccinia and Trichoxanthes have been well-documented to understand the genetics of sex determination (Volz and Renner 2008;Ming et al 2011;Bhowmick et al 2016;Mohanty et al 2017), comparatively little or no interest has been attributed to the sexual development in Momordica, a genus with multiple perennial species that has undergone seven transitions from dioecy to monoecy (Schaefer and Renner 2010). Momordica dioica (spiny gourd) is a prominent dioecious member of this genus with a small genome size and an incipient set of homomorphic sex chromosomes that could be used as a sculpt for studying sexual phenotypes.…”

Section: Introductionmentioning

confidence: 99%

Molecular cloning, characterization and expression analysis of MADS-box genes associated with reproductive development in Momordica dioica Roxb.

Mohanty

Joshi

2018

3 Biotech

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The repertoire and functions of MADS-box family transcription factors (TFs) largely remains unexplored with respect to floral organogenesis of Roxb. Degenerative PCR followed by rapid amplification of cDNA ends was employed in the present study to clone and characterize 17 MADS-box genes (designated as to ) from the floral buds of The cloned genes were clustered into three subgroups (11 MIKC, 4 MIKC* and 2 Mα) based on phylogenetic relationships with the MADS-box genes from and. Southern hybridization showed that all the isolated genes were represented by single copy locus in the genome. Gene structure analysis revealed 1-8 exons in-box genes with the number of exons in MIKC greatly exceeding from that in M-type genes. Motif elicitation of the -box genes indicated the presence of additional domains with MIKC type, suggesting that they had more complex structures. Expression analysis of genes in six transcriptome suggested that, 11 MIKC-type genes are associated with floral homeotic functions, 4 MIKC*-type genes ( to ) controlled the growth of male gametophyte, while the two-type genes ( and ) played significant role in female gametogenesis and seed development. Overall, these are the first set of MADS-box genes from exhibiting a differential expression pattern during floral development. The results from this study will provide valuable information for further functional studies of candidate MADS-box genes in the sexual dimorphism of this economically important dioecious cucurbit.

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Transcriptome profiling of the floral buds and discovery of genes related to sex-differentiation in the dioecious cucurbit Coccinia grandis (L.) Voigt

Cited by 22 publications

References 67 publications

De Novo assembly, characterization and development of EST-SSRs from Bletilla striata transcriptomes profiled throughout the whole growing period

De Novo assembly, characterization and development of EST-SSRs from Bletilla striata transcriptomes profiled throughout the whole growing period

Impact of Repetitive Elements on the Y Chromosome Formation in Plants

Molecular cloning, characterization and expression analysis of MADS-box genes associated with reproductive development in Momordica dioica Roxb.

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