Characterization of Leaf Transcriptome in <i>Banksia Hookeriana</i>

Lim, Seng Han; D’Agui, Haylee M.; Enright, Neal J.; He, Tianhua

doi:10.1016/j.gpb.2016.11.001

Cited by 9 publications

(6 citation statements)

References 51 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…There are few genomic resources for either macadamia or within the Proteaceae. Transcriptomic data are available for Macadamia ( Chabika et al 2020 ) and other Proteaceae genera including Banksia ( Lim et al 2017 ), Grevillea ( Damerval et al 2019 ) , Protea ( Akman et al 2016 ) and Gevuina ( Ostria-Gallardo et al 2016 ) , and have been utilized to help to understand the evolution of floral architecture ( Damerval et al 2019 ) and variation in locally adaptive traits ( Akman et al 2016 ). Recent genome wide association studies in macadamia have identified markers associated with commercially important traits ( O’Connor et al 2020 ) but their location and context in the genome is unknown.…”

mentioning

confidence: 99%

Chromosome-Scale Assembly and Annotation of the Macadamia Genome (Macadamia integrifolia HAES 741)

Nock

Baten

Mauleon

et al. 2020

G3 Genes|Genomes|Genetics

View full text Add to dashboard Cite

Macadamia integrifolia is a representative of the large basal eudicot family Proteaceae and the main progenitor species of the Australian native nut crop macadamia. Since its commercialisation in Hawaii fewer than 100 years ago, global production has expanded rapidly. However, genomic resources are limited in comparison to other horticultural crops. The first draft assembly of M. integrifolia had good coverage of the functional gene space but its high fragmentation has restricted its use in comparative genomics and association studies. Here we have generated an improved assembly of cultivar HAES 741 (4,094 scaffolds, 745 Mb, N50 413 kb) using a combination of Illumina paired and PacBio long read sequences. Scaffolds were anchored to 14 pseudo-chromosomes using seven genetic linkage maps. This assembly has improved contiguity and coverage, with >120 Gb of additional sequence. Following annotation, 34,274 protein-coding genes were predicted, representing 90% of the expected gene content. Our results indicate that the macadamia genome is repetitive and heterozygous. The total repeat content was 55% and genome-wide heterozygosity, estimated by read mapping, was 0.98% or an average of one SNP per 102 bp. This is the first chromosome-scale genome assembly for macadamia and the Proteaceae. It is expected to be a valuable resource for breeding, gene discovery, conservation and evolutionary genomics.

show abstract

mentioning

confidence: 99%

Chromosome-Scale Assembly and Annotation of the Macadamia Genome (Macadamia integrifolia HAES 741)

Nock

Baten

Mauleon

et al. 2020

G3 Genes|Genomes|Genetics

View full text Add to dashboard Cite

show abstract

“…Transcriptomic data from Proteaceae species are scarce and have mostly been obtained from leaves for specific purposes: in Leucadendron to derive phylogenetic markers (Tonnabel et al, 2014), in Protea repens to study population differentiation in relation to local adaptation (Akman et al, 2016), in Banksia hookeriana to derive SSR markers (Lim et al, 2017) and in Gevuina avellana to study heteroblastic development under different light conditions (Ostria-Gallardo et al, 2016). In Macadamia integrifolia , a reference transcriptome was built from flowers, shoots and leaves, in parallel to a draft genome (Nock et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

Unraveling the Developmental and Genetic Mechanisms Underpinning Floral Architecture in Proteaceae

et al. 2019

View full text Add to dashboard Cite

Proteaceae are a basal eudicot family with a highly conserved floral groundplan but which displays considerable variation in other aspects of floral and inflorescence morphology. Their morphological diversity and phylogenetic position make them good candidates for understanding the evolution of floral architecture, in particular the question of the homology of the undifferentiated perianth with the differentiated perianth of core eudicots, and the mechanisms underlying the repeated evolution of zygomorphy. In this paper, we combine a morphological approach to explore floral ontogenesis and a transcriptomic approach to access the genes involved in floral organ identity and development, focusing on Grevillea juniperina, a species from subfamily Grevilleoideae. We present developmental data for Grevillea juniperina and three additional species that differ in their floral symmetry using stereomicroscopy, SEM and High Resolution X-Ray Computed Tomography. We find that the adnation of stamens to tepals takes place at early developmental stages, and that the establishment of bilateral symmetry coincides with the asymmetrical growth of the single carpel. To set a framework for understanding the genetic basis of floral development in Proteaceae, we generated and annotated de novo a reference leaf/flower transcriptome from Grevillea juniperina. We found Grevillea homologs of all lineages of MADS-box genes involved in floral organ identity. Using Arabidopsis thaliana gene expression data as a reference, we found homologs of other genes involved in floral development in the transcriptome of G. juniperina. We also found at least 21 class I and class II TCP genes, a gene family involved in the regulation of growth processes, including floral symmetry. The expression patterns of a set of floral genes obtained from the transcriptome were characterized during floral development to assess their organ specificity and asymmetry of expression.

show abstract

“…Raw reads produced from the sequencing were scrutinized for quality in terms of total raw reads, total clean reads, Q20 percentage (proportion of nucleotides (NTs) with quality value > 20), N percentage (proportion of unknown NTs in clean reads), and GC percentage. Sequence reads with adaptors of unknown NTs (numbering > 5%) or low quality (reads with quality values ≤ 10), representing more than 20%, were discarded by filter_fq software, and only high-quality sequence reads were retained for assembly [52]. The Trinity software package was used to assemble the data into unigene collections from each of the 12 cDNA libraries [53].…”

Section: Methodsmentioning

confidence: 99%

Comparative transcriptome analysis provides key insights into seedling development in switchgrass (Panicum virgatum L.)

Zhang

Sun

Wang

et al. 2019

Biotechnol Biofuels

View full text Add to dashboard Cite

Background Switchgrass ( Panicum virgatum L.), a warm-season perennial C4 plant, can be used as a forage plant, a soil and water conservation plant, a windbreak plant, and as a good source of biofuels and alternative energy with low planting costs. However, switchgrass exhibits low rates of seedling development compared to other crops, which means it is typically out-competed by weeds. There is a large variation in seedling development rates among different plantlets in switchgrass, which limits its usefulness for large-scale cultivation. Little is currently known about the molecular reasons for slow seedling growth. Results Characterization of the seedling development process via growth indices indicated a relatively stagnant growth stage in switchgrass. A total of 678 differentially expressed genes (DEGs) were identified from the comparison of transcriptomes from slowly developed (sd) and rapidly developed (rd) switchgrass seedlings. Gene ontology and pathway enrichment analysis showed that DEGs were enriched in diterpenoid biosynthesis, thiamine metabolism, and circadian rhythm. Transcription factor enrichment and expression analyses showed MYB-related, bHLH and NAC family genes were essential for seedling growth. The transcriptome results were consistent with those of quantitative real-time polymerase chain reaction. Then, the expression profiles of maize and switchgrass were compared during seedling leaf development. A total of 128 DEGs that play key roles in seedling growth were aligned to maize genes. Transcriptional information and physiological indices suggested that several genes involved in the circadian rhythm, thiamine metabolism, energy metabolism, gibberellic acid biosynthesis, and signal transduction played important roles in seedling development. Conclusions The seedling development process of switchgrass was characterized, and the molecular differences between slowly developed and rapidly developed seedlings were discussed. This study provides new insights into the reasons for slow seedling development in switchgrass and will be useful for the genetic improvement of switchgrass and other crops. Electronic supplementary material The online version of this article (10.1186/s13068-019-1534-4) contains supplementary material, which is available to authorized users.

show abstract

Characterization of Leaf Transcriptome in Banksia Hookeriana

Cited by 9 publications

References 51 publications

Chromosome-Scale Assembly and Annotation of the Macadamia Genome (Macadamia integrifolia HAES 741)

Chromosome-Scale Assembly and Annotation of the Macadamia Genome (Macadamia integrifolia HAES 741)

Unraveling the Developmental and Genetic Mechanisms Underpinning Floral Architecture in Proteaceae

Comparative transcriptome analysis provides key insights into seedling development in switchgrass (Panicum virgatum L.)

Contact Info

Product

Resources

About