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Moso bamboo is well-known for its rapid-growth shoots and widespread rhizomes. However, the regulatory genes of these two processes are largely unexplored. GATA transcription factors regulate many developmental processes, but their roles in moso bamboo height control and rhizome development remains unexplored. Here, thirty-one bamboo GATA factors (PeGATAs) were identified, which are evolutionarily closer to rice than Arabidopsis, and their gene expression patterns were analyzed in bamboo development and phytohormone response with bioinformatics and molecular methods. Interestingly, PeGATAs could only be classified into three groups. Phytohormone responsive cis-elements were found in PeGATA promoters and the expression profiles showed that PeGATA genes might respond to gibberellin acid and abscisic acid but not to auxin at the transcriptional level. Furthermore, PeGATA genes have a tissue-specific expression pattern in bamboo rhizomes. Interestingly, most PeGATA genes were down-regulated during the rapid-growth of bamboo shoots. In addition, over-expressing one of the PeGATA genes, PeGATA26, significantly repressed the primary root length and plant height of transgenic Arabidopsis plants, which may be achieved by promoting the gibberellin acid turnover. Overall, our results provide insight into the function of GATA transcription factors in bamboo, and into genetic resources for engineering plant height.

Spartina alterniflora (Spartina) is the only halophyte in the salt marsh. However, the molecular basis of its high salt tolerance remains elusive. In this study, we used Pacific Biosciences (PacBio) full-length single-molecule long-read sequencing and RNA-seq to elucidate the transcriptome dynamics of high salt tolerance in Spartina by salt gradient experiments. High-quality unigenes, transcription factors, non-coding RNA and Spartina-specific transcripts were identified. Co-expression network analysis found that protein kinase-encoding genes (SaOST1, SaCIPK10 and SaLRRs) are hub genes in the salt tolerance regulatory network. High salt stress induced the expression of transcription factors but repressed the expression of long non-coding RNAs. The Spartina transcriptome is closer to rice than Arabidopsis, and a higher proportion of transporter and transcription factor-encoding transcripts have been found in Spartina. Transcriptome analysis showed that high salt stress induced the expression of carbohydrate metabolism, especially cell-wall biosynthesis-related genes in Spartina, and repressed its expression in rice. Compared with rice, high salt stress highly induced the expression of stress response, protein modification and redox-related gene expression and greatly inhibited translation in Spartina. High salt stress also induced alternative splicing in Spartina, while differentially expressed alternative splicing events associated with photosynthesis were overrepresented in Spartina but not in rice. Finally, we built the SAPacBio website for visualizing full-length transcriptome sequences, transcription factors, ncRNAs, salt-tolerant genes and alternative splicing events in Spartina. Overall, this study suggests that the salt tolerance mechanism in Spartina is different from rice in many aspects and is far more complex than expected.

18 Spartina alterniflora (Spartina) is the only halophyte in the salt marsh. However, the 19 molecular basis of its high salt tolerance remains elusive. In this study, we used 20 PacBio full-length single molecule long-read sequencing and RNA-seq to elucidate 21 the transcriptome dynamics of high salt tolerance in Spartina by salt-gradient 22 Spartina. Overall, this study sheds light on the high salt tolerance mechanisms of 34 monocotyledonous-halophyte and demonstrates the potential of Spartina genes for 35 engineering salt-tolerant plants. 36 Running title: Spartina transcriptome under salt stress 37 Keywords: Spartina alterniflora; high salt tolerance; ion transporter; protein kinase; 38 regulatory hub genes; alternative splicing; single molecule real-time sequencing 39 40 41 42 43 44 45 46 47 48 alterniflora exhibits a delicate ion exclusion system from physiology aspects to 66 survive hash saline environment and it is a good model plant to study high salt 67 tolerance. However, the molecular basis of salt tolerance in Spartina alterniflora 68 remains unexplored, and the post-transcriptional regulation of high salt tolerance has 69 not been characterized in plants. 70

18 · Background 19Moso bamboo is well-known for its rapid-growth shoots and widespread rhizomes. 20However, the regulatory genes of these two processes are largely unexplored. 21 GATA factors regulate many developmental processes, but its role in plant height 22 control and rhizome development remains unclear. 23 · Results 24Here, we found that bamboo GATA factors (PeGATAs) are involved in the 25 growth regulation of bamboo shoots and rhizomes. Bioinformatics and 26 evolutionary analysis showed that there are 31 PeGATA factors in bamboo, which 27 can be divided into three subfamilies. Light, hormone, and stress-related 28 cis-elements were found in the promoter region of the PeGATA genes. Gene 29 expression of 12 PeGATA genes was regulated by phytohormone-GA but there 30 was no correlation between auxin and PeGATA gene expression. More than 27 31PeGATA genes were differentially expressed in different tissues of rhizomes, and 32 almost all PeGATAs have dynamic gene expression level during the rapid-growth 33 3 of bamboo shoots. These results indicate that PeGATAs regulate rhizome 34 development and bamboo shoot growth partially via GA signaling pathway. In 35 addition, PeGATA26, a rapid-growth negative regulatory candidate gene 36 modulated by GA treatment, was overexpressed in Arabidopsis, and 37 over-expression of PeGATA26 significantly repressed Arabidopsis primary root 38 length and plant height. The PeGATA26 overexpressing lines were also resistant 39 to exogenous GA treatment, further emphasizing that PeGATA26 inhibits plant 40 height from Arabidopsis to moso bamboo via GA signaling pathway. 41 · Conclusions 42Our results provide an insight into the function of GATA transcription factors in 43 regulating shoot rapid-growth and rhizome development, and provide genetic 44 resources for engineering plant height. 45Running title: GATA family in moso bamboo 46

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