DOI: 10.5061/dryad.tqjq2bw6s
title: Transcriptomic findings light on mechanisms of marine and terrestrial evolutionary adaptation of Rhizophoraceae plants

description: Rhizophoraceae has 2 terrestrial genera and 4 marine genera. The
 intertidal zone in which marine mangroves are located is known for its low
 oxygen and high salinity. Marine and terrestrial genera have evolved
 distinct adaptive characteristics, among which viviparous reproduction is
 the most unique. To investigate the genetic foundations difference
 underlying the adaptive mechanisms of marine–terrestrial genera, we
 selected two species from Rhizophoraceae. Kandelia obovata is marine and
 viviparous, and Carallia brachiata is terrestrial and non-viviparous. We
 compared their transcriptome of 8 tissues (root, stem, leaf, flower,
 ovule, fruit, seed, embryo) and found that the mature reproductive organs
 (fruit, seed, embryo) of K. obovata did not reduce metabolic activity
 compared to C. brachiata. The reproductive organs of K. obovata were
 regulated by the same gene set as vegetative organs. This contrasted with
 C. brachiata. Eight kinds of hormone transduction genes were up-regulated
 in the seed of K. obovata. Finally, and most importantly, the
 transcriptional factors AP2 and ARF families were significantly more
 expressed in the reproductive organs of K. obovata than in those of C.
 brachiata. At the same time, the ERF family was more expressed in its
 roots. The findings suggested that the hormone transduction may contribute
 to viviparous initiation. Transcriptional factors were quite crucial for
 mangroves' adaptation to wetlands.
description: Reverse transcription (RT) was performed with 1 μg total RNA
 isolated from three independent biological replicates per species using 5X
 All-In-One RT MasterMix (ABM, Canada). The reaction procedure is as
 follows: incubate at 25 °C for 10 minutes, then incubate at 42 °C for
 another 15 minutes, and inactivate the reaction at 85 °C for 5 minutes.
 First-strand cDNA was diluted to 200 ng/μL as a quantitative template. The
 relative quantification was done by ChamQTM Universal SYBR® qPCR Master
 Mix (Vazyme, China). The reaction system was 10 μL 2 x SYBR Green PCR Mix,
 0.5 μL upstream primer, 0.5 μL downstream primer, 8 μL H2O. RT-qPCR was
 performed on the above mixture, and the reaction procedure was as follows:
 95 °C, 30 s; 95 °C, 10 s; 58 °C, 10 s; 72 °C, 20 s, and 40 cycles.
 <em>Actin</em> was selected for the reference gene. The
 relative expression of the target gene was calculated by the 2−ΔΔCt
 method.
description: # **Transcriptomic findings light on mechanisms of marine and terrestrial
 evolutionary adaptation of Rhizophoraceae plants** --- We have submitted
 our raw data (**Raw data of RT-qPCR.xls**), which includes three shifts
 and gene validation in roots (**Raw data of roots**), seeds (**Raw data of
 seeds**), and statistical analysis (**t-test**). ## Descriptions ### **Raw
 data of roots** and **Raw data of seeds** * *Sample Name*: CB, *Carallia
 brachiata*; KO, *Kandelia obovata*. Arabic numerals represent biological
 repetition. * *Gene*: The name of the verified gene in CB and KO. * *CT*:
 Cycle Threshold refers to the number of cycles required for the initial
 fluorescence value to reach the threshold. * *Ct Mean*: Average of the CT
 of three biological repetitions * *Ct SD*: Sample standard deviation of CT
 of three biological repetitions ### **t-test** * Highlighted cells show
 the gene name and the following are the results of the t-test. * Column A
 and Column B are the tissues of root or seed in two species CB and KO. *
 In the *P*-value summary, ns, and one, two, or three stars (asterices)
 indicate different degrees of difference. They are marked with such
 symbols when *P*&gt;0.05, *P*≤0.05, *P*≤0.01, and *P*≤0.001, respectively.