Transcriptomic findings light on mechanisms of marine and terrestrial evolutionary adaptation of Rhizophoraceae plants

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 ..., 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. Actin was selected for the reference gene. The relative expression of the target gene was calculated by the 2−ΔΔCt method., , # **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 tis...

红树科（Rhizophoraceae）包含2个陆生属和4个海生属。海生红树所处的潮间带以低氧和高盐为显著特征。海生属与陆生属演化出了截然不同的适应性特征，其中胎生繁殖最为独特。为探究海生-陆生属适应性机制背后的遗传基础差异，我们从红树科中选取了两个物种：海生胎生的秋茄（Kandelia obovata）和陆生非胎生的竹节树（Carallia brachiata）。我们对比了二者8种组织（根、茎、叶、花、胚珠、果实、种子、胚胎）的转录组（transcriptome），发现秋茄的成熟繁殖器官（果实、种子、胚胎）相较于竹节树并未降低代谢活性。秋茄的繁殖器官与营养器官受同一套基因调控，这与竹节树形成鲜明对比。8类激素转导基因在...中上调（原文此处未完整）。
使用加拿大ABM公司的5X All-In-One RT MasterMix试剂盒，对每个物种3个独立生物学重复（biological replicates）样本中提取的1μg总RNA进行逆转录（RT）。反应程序如下：25°C孵育10分钟，随后42°C孵育15分钟，最后85°C灭活5分钟。将第一链cDNA稀释至200 ng/μL作为定量模板。使用中国Vazyme公司的ChamQTM Universal SYBR® qPCR Master Mix试剂盒进行相对定量。反应体系为：10μL 2×SYBR Green PCR Mix、0.5μL上游引物、0.5μL下游引物、8μL H₂O。对上述混合液进行RT-qPCR反应，程序如下：95°C预变性30秒；95°C变性10秒、58°C退火10秒、72°C延伸20秒，循环40次。选择肌动蛋白（Actin）作为内参基因，采用2⁻ΔΔCt法计算目标基因的相对表达量。

# **红树科植物海生-陆生演化适应机制的转录组学研究发现**

---

我们已提交原始数据（**Raw data of RT-qPCR.xls**），包括三个批次的数据、根组织基因验证数据（**Raw data of roots**）、种子组织基因验证数据（**Raw data of seeds**）及统计分析结果（**t-test**）。

## Descriptions

### **Raw data of roots** and **Raw data of seeds**

* **Sample Name**：CB代表*Carallia brachiata*；KO代表*Kandelia obovata*；阿拉伯数字表示生物学重复。
* **Gene**：CB和KO中验证的基因名称。
* **CT**：循环阈值（Cycle Threshold），指初始荧光值达到阈值所需的循环次数。
* **Ct Mean**：三个生物学重复CT值的平均值。
* **Ct SD**：三个生物学重复CT值的样本标准差。

### **t-test**

* 高亮单元格显示基因名称，其后为t检验结果。
* Column A和Column B为组织...（原文此处未完整）