Construction of a Full-Length cDNA Library and Analysis of Expressed Sequence Tags from Inflorescence of Apomictic Sabaigrass (Eulaliopsis binata)

Abstract

Eulaliopsis binata, which is a close relative of cereal crops, was recognized as an important research material owing to its high frequency of apospory and autonomous endosperm formation. However, little information is known about its genomics and regulatory pathway participating in reproductive development. For the first step to understand molecular basis in sabaigrass (E. binata), a SMART complementary DNA library from the inflorescence tissue was constructed and characterized. The titers of original and amplified libraries were 5.53×10 6 and 1.49×10 10 pfu/ml, respectively. The percentage of recombinants was 96% in the original library. Analysis of sequencing results of 398 out of 437 randomly picked clones showed that 271 (68.1%) expressed sequence tags (ESTs) exhibited significant similarity with known putative functional nucleotide sequences in the GenBank databases, 25 (6.3%) ESTs have significant matches with hypothetical proteins, putative proteins, and unknown proteins, and the other 25.6% ESTs had no significant similarity to sequences in the public databases. Based on molecular function of GO annotation, the four most abundant terms are nucleotide binding, hydrolase activity, ion binding, and protein binding, and these genes were involved in 61 different pathways using the Kyoto Encyclopedia of Genes and Genomes pathway analysis. Besides, simple sequence repeats detection in 398 ESTs was carried out, and several genes were chosen to perform expression analysis. This report represents a first step in expanding molecular-genetic analyses in E. binata and can be used to optimally mine useful information from a relatively small data set.

Construction of cDNA Library of <i>Hansenula </i><i>an</i><i>omala</i>

“…The Extraction and Detection of Total RNA. The ground in liquid nitrogen and Trizol methods [12] were used to extract RNA, each 1µl RNA were taken for determination of its OD value and electrophoresis, the remainings were set at -80℃.…”

Construction of a full-length cDNA library and analysis of expressed sequence tags in white jute (Corchorus capsularis L.)

“…Instead of using traditional breeding methods, jute breeders and biologists are now turning their attention to use molecular tools to improve agronomic traits (Khatun, 2007). However, many potentially fruitful research avenues, especially large-scale gene expression surveys and development of molecular genetic markers have been limited by a lack of sequence information in public databases (Zhang et al, 2011a). For a non-model species such as jute, with no prior genomic knowledge and resources (only 2,036 nucleotide and 54 EST sequences in NCBI database) (Kundu et al, 2015), it is critical to isolate, identify and understand the expressed sequences, with a long term goal of genetically modifying jute.…”

“…Expressed sequence tag (EST) projects provide a very useful and quick means of accessing gene sequence and expression information (Manickavelu et al, 2012). Some reports have proven that projects based on ESTs are powerful tools for both the analysis of gene expression patterns in a given tissue or at specific developmental stages (Chen et al, 2012;Tran et al, 2011;Wang et al, 2011b;Yang et al, 2009b;Zhang et al, 2011a). Moreover, ESTs from complementary DNA (cDNA) clones are inexpensive and efficient gene discovery tools (Wang et al, 2011a;Xiao et al, 2011;Yamagishi et al, 2011).…”

BbrizAGL6 Is Differentially Expressed During Embryo Sac Formation of Apomictic and Sexual Brachiaria brizantha Plants

“…Isolating and characterising genes that are putatively related to the determination of sporophytic and gametophytic fates of the ovule in apomictic and sexual plants can contribute to understanding the molecular basis of these modes of reproduction. Gene expression information is being built in the female reproductive organs, where the main differences between apomictic and sexual plants occur (Pessino et al 2001;Rodrigues et al 2003;Polegri et al 2010;Sharbel et al 2010;Zhang et al 2012). In B. brizantha, a differential pattern of expression in developing ovaries of apomictic and sexual plants was detected by macroarray analysis (Silveira et al 2012).…”