Revealing the full-length transcriptome of caucasian clover rhizome development

Background Caucasian clover (Trifolium ambiguum M. Bieb.) is a strongly rhizomatous, low-crowned perennial leguminous and ground-covering grass. The species may be used as an ornamental plant and is resistant to cold, arid temperatures and grazing due to a well-developed underground rhizome system and a strong clonal reproduction capacity. However, the posttranscriptional mechanism of the development of the rhizome system in caucasian clover has not been comprehensively studied. Additionally, a reference genome for this species has not yet been published, which limits further exploration of many important biological processes in this plant. Result We adopted PacBio sequencing and Illumina sequencing to identify differentially expressed genes (DEGs) in five tissues, including taproot (T1), horizontal rhizome (T2), swelling of taproot (T3), rhizome bud (T4) and rhizome bud tip (T5) tissues, in the caucasian clover rhizome. In total, we obtained 19.82 GB clean data and 80,654 nonredundant transcripts were analysed. Additionally, we identified 78,209 open reading frames (ORFs), 65,227 coding sequences (CDSs), 58,276 simple sequence repeats (SSRs), 6821 alternative splicing (AS) events, 2429 long noncoding RNAs (lncRNAs) and 4501 putative transcription factors (TFs) from 64 different families. Compared with other tissues, T5 exhibited more DEGs, and co-upregulated genes in T5 are mainly annotated as involved in phenylpropanoid biosynthesis. We also identified betaine aldehyde dehydrogenase (BADH) as a highly expressed gene-specific to T5. A weighted gene co-expression network analysis (WGCNA) of transcription factors and physiological indicators were combined to reveal 11 hub genes (MEgreen-GA3), three of which belong to the HB-KNOX family, that are up-regulated in T3. We analysed 276 DEGs involved in hormone signalling and transduction, and the largest number of genes are associated with the auxin (IAA) signalling pathway, with significant up-regulation in T2 and T5. Conclusions This study contributes to our understanding of gene expression across five different tissues and provides preliminary insight into rhizome growth and development in caucasian clover.

Revealing the full-length transcriptome of caucasian clover rhizome development

Background: Caucasian clover (Trifolium ambiguum M. Bieb.) is a strongly rhizomatous, low-crowned perennial leguminous and ground-covering grass. The species may be used as an ornamental plant and is resistant to cold, arid temperatures and grazing due to a well-developed underground rhizome system and a strong clonal reproduction capacity. However, the posttranscriptional mechanism of the development of the rhizome system in caucasian clover has not been comprehensively studied. Additionally, a reference genome for this species has not yet been published, which limits further exploration of many important biological processes in this plant. Result: We adopted PacBio Sequencing and Illumina Sequencing to identify differentially expressed transcripts in five tissues taproot (T1), horizontal rhizome (T2), swelling of taproot (T3), rhizome bud (T4) and rhizome bud tip (T5) of the caucasian clover rhizome. In total, we obtained 19.82 GB clean data and 80,654 nonredundant transcripts were analysed. Additionally, we identified 78,209 open reading frames (ORFs), 65,227 coding sequences (CDSs), 58,276 simple sequence repeats (SSRs), 6,821 alternative splicing (AS) sites, 24,29 long noncoding RNAs (lncRNAs) and 4,501 putative transcription factors (TFs) from 64 different families. Compared with other tissues, T5 exhibited more differentially expressed genes, and co-upregulated genes in T5 are mainly annotated as involved in phenylpropanoid biosynthesis. We also identified betaine aldehyde dehydrogenase (BADH) as a highly expressed gene-specific to T5. A weighted gene co-expression network analysis (WGCNA) cluster analysis of transcription factors and physiological indicators were combined to reveal 11 candidate genes (MEgreen-GA3), three of which belong to the HB-KNOX family, that are up-regulated in T3. We analysed 276 differential transcripts involved in hormone signaling and transduction, and the largest number of transcripts are associated with the IAA signaling pathway, with significant up-regulation in T2 and T5. Conclusions: Taken together, this study contributes to our understanding of gene expression across five different tissues and provides preliminary insight into rhizome growth and development in caucasian clover.

Revealing the full-length transcriptome of caucasian clover rhizome development

Background: Caucasian clover (Trifolium ambiguum M.Bieb.) is a strongly rhizomatous, low-crowned perennial leguminous and ground-covering grass. The species may be used as an ornamental plant and is resistant to cold, arid temperatures and grazing due to a well-developed underground rhizome system and a strong clonal reproduction capacity. However, the posttranscriptional mechanism of the development of the rhizome system in caucasian clover has not been comprehensively studied. Additionally, a reference genome for this species has not yet been published, which limits further exploration of many important biological processes in this plant. Result: We adopted PacBio Sequencing and Illumina Sequencing to identify differentially expressed transcripts in five tissues taproot (T1), horizontal rhizome (T2), swelling of taproot (T3), rhizome bud (T4) and rhizome bud tip (T5) of the caucasian clover rhizome. In total, we obtained 19.82 GB clean data and 80,654 nonredundant transcripts were analyzed. Additionally, we identified 78,209 open reading frames (ORFs), 65,227 coding sequences (CDSs), 58,276 simple sequence repeats (SSRs), 6,821 alternative splicing (AS) sites, 24,29 long noncoding RNAs (lncRNAs) and 4,501 putative transcription factors (TFs)from 64 different families. Compared with other tissues, T5 exhibited more differentially expressed genes, and co-upregulated genes in T5 are mainly annotated as involved in phenylpropanoid biosynthesis. We also identified betaine aldehyde dehydrogenase (BADH) as a highly expressed gene specific to T5. WGCNA cluster analysis of transcription factors and physiological indicators were combined to reveal 11 candidate genes (MEgreen-GA3), three of which belong to the HB-KNOX family, that are up-regulated in T3. We analyzed 276 differential transcripts involved in hormone signaling and transduction, and the largest number of transcripts are associated with the IAA signaling pathway, with significant upregulation in T2 and T5. Conclusions: Taken together, this study contributes to our understanding of gene expression across five different tissues and provides preliminary insight into rhizome growth and development in caucasian clover.

The new fern genus Calciphilopteris (Pteridaceae)

A new genus of Pteridaceae subfamily Cheilanthoideae is established for what has long been known as Doryopteris ludens. The newly erected genus is named Calciphilopteris in reference to its substrate specificity to limestone. Calciphilopteris can be found throughout Southeast Asia, from Indo-China to New Guinea and Australia. New combinations are established for the four known species (Calciphilopteris alleniae, C. ludens, C. papuana and C. wallichii). Calciphilopteris is characterized by having a horizontal rhizome, semi-clathrate scales, indumentum on the petiole and lamina usually with fibrils and/or semi- to non-clathrate scales, and sporangia with 32 echinate or cristate spores.

Occurrence and fruit and seed biology of Halophila tricostata Greenway (Hydrocharitaceae)

Halophila tricostata Greenway appears to be endemic to eastern Queensland, Australia, and occurs between 14�11'S and 23�45's. It was found at depths from 1.4 to 30 m in well sheltered habitats, including in shallow coastal sites near mangrove-lined estuaries, on the lee side of continental and coral- reef islands, and on some commercial prawn-trawling grounds within the Great Barrier Reef lagoon. It grows on predominantly fine mud substratum in small monospecific meadows or mixed with other tropical seagrasses, mostly other Halophila species. Field observations indicate that H. tricostata is an annual angiosperm and produces an estimated 70 000 seeds m-2 year-1. Halophila tricostata is dioecious. The plant has a horizontal rhizome bearing an erect shoot with eight to twelve nodes and a root at each rhizome node. Except at the first two or three nodes, the mature plants produce a reproductive organ at each node of their rarely branched erect shoot. The reproductive organs and fruits develop and mature acropetally along the erect shoot. There are 24-60 seeds, with a mean of 41 seeds, per fruit. The seed has a coiled embryo protected by a cotyledon, and an enlarged hypocotyl. The hypocotyl acts as a nutrient store and contains starch, protein and lipid. The seed covering consists of pericarp remains and two thin cuticular layers of seed coat. The surface of the seed covering has numerous fine protrusions. The seed covering becomes loose and is discarded during germination, exposing the hypocotyl. The surface of the hypocotyl develops hair-like unicellular structures during seedling development. The majority of the seeds begin to germinate at 26-28�C after two weeks of culturing, but germination is not synchronized. The culturing of H. tricostata seedlings beyond the three-leaf stage was not successful.