3/16/2023 0 Comments Clc genomics workbench 21In the latter case, when isolated cotyledons are placed in culture, adaxial epidermal cells trans-differentiate to become functional epidermal TCs ( Farley et al., 2000 Dibley et al., 2009). faba is also widely used in plant physiology research to study such processes as guard cell dynamics in leaves ( Fukuda et al., 1998 Fellè et al., 2000), transport processes in phloem ( Thorpe et al., 2010 Hafke et al., 2013), and importantly for this study, transfer cell (TC) development in cotyledons ( Offler et al., 2003). In addition to its importance as a crop species worldwide, V. Vicia faba (L.) is an important cool-season grain legume species used widely for human nutrition, fodder for livestock and as a rotation crop for nitrogen replenishment of soils ( Torres et al., 1993 El-Rodeny et al., 2014). Chen et al., 2014), cell wall synthesizing enzymes in paper mulberry ( Xianjun et al., 2014), biomass production in Panicum hallii ( Meyer et al., 2012), and plant sex determination in cucumber ( Guo et al., 2010). In combination with de novo assembly of novel transcriptomes, RNA-Seq provides a platform for transcript profiling in these non-annotated species, thus enabling a deeper understanding at the transcriptional level of diverse but little studied biological processes in plants, such as fiber development in ramie ( Boehmeria nivea L. De novo assembly of transcriptomes from such species has enabled gene discovery and marker identification in a wide variety of non-genome-sequenced agricultural species such as common wheat ( Duan et al., 2012), peanut ( Zhang et al., 2012), and rubber tree ( Mantello et al., 2014), but especially in crop legumes such as pea ( Franssen et al., 2011), yellow lupin ( Parra-González et al., 2012), lentils ( Verma et al., 2013), and chick pea ( Garg et al., 2011a, b), which are important to agriculture but genetic studies have been limited due to their often large genomes. The introduction of RNA sequencing (RNA-Seq) has widened the use of plant species for molecular genetic analyses beyond those for which full genome sequences are available. This genome-wide transcriptome map therefore provides a valuable tool for future transcript profiling of epidermal TC trans-differentiation, and also enriches the genetic resources available for this important legume crop species. faba cDNAs held in GenBank, including transcripts previously identified as being specifically expressed in epidermal cells across TC trans-differentiation. The assembly was validated against known V. Assembly using a De-Bruijn graph-based approach generated 21,297 contigs, of which 80.6% were successfully annotated against GO terms. Illumina paired-end sequencing of total RNA pooled from different tissues and different stages, including isolated cotyledons induced to form epidermal TCs, generated 69.5 M reads, of which 65.8 M were used for assembly following trimming and quality control. To provide a resource for future transcript profiling of epidermal TC differentiation, we have undertaken de novo assembly of a genome-wide transcriptome map for V. 13 Gb), however, and limited genomic information is available for this species. Adaxial epidermal cells of isolated cotyledons can be induced to form functional TCs, thus providing a valuable experimental system to investigate genetic regulation of TC trans-differentiation. Many TCs are formed by trans-differentiation from differentiated cells at apoplasmic/symplasmic boundaries in nutrient transport. TCs are specialized nutrient transport cells in plants, characterized by invaginated wall ingrowths with amplified plasma membrane surface area enriched with transporter proteins that facilitate nutrient transfer. Vicia faba (L.) is an important cool-season grain legume species used widely in agriculture but also in plant physiology research, particularly as an experimental model to study transfer cell (TC) development. Centre for Plant Science, School of Environmental and Life Sciences, The University of Newcastle, Newcastle, NSW, Australia.
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