Comparative RNA-Seq analysis of <i>Betula platyphylla</i> under low and high temperature stresses

Ritonga, Faujiah Nurhasanah; Chen, Song; Indriani, Fitri; Song, Runxian; Zhang, Xiang; Lan, Xingguo; Chen, Su

doi:10.1590/01047760202329013147

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SILVICULTURE • CERNE 29 • 2023 • https://doi.org/10.1590/01047760202329013147 copy

Comparative RNA-Seq analysis of Betula platyphylla under low and high temperature stresses

Authorship SCIMAGO INSTITUTIONS RANKINGS

ABSTRACT

Background:

Betula platyphylla Sukaczev is one of important tree species due to its ecological and economic value. It is a cold-tolerant tree species which also faces heat stress during summer. In the current study, RNA-Seq profiling of two-month-old B. platyphylla seedlings were conducted utilizing the MGISEQ-2000 platform.

Results:

In total, 856,347,961 clean reads were obtained from 26 RNA-Seq libraries. Totally, 822,552,820 reads were successfully mapped to B. platyphylla reference genome. Further, a total of 360 and 264 DEGs were discovered under cold and heat exposure, respectively, while a total of 104 DEGs were identified under both cold and heat exposure. It was found that several pathways including response to cold, response to heat, response to temperature stimulus, response to stress, lipid metabolic, jamonic acid and ethylene, even developmental processes were significantly enriched in GO enrichment analysis of cold and heat stress in biological process term. Several transcription factors (TFs), including MYB66, CBF2, bHLH96and bZIP7 take a pivotal role in response to temperature stresses. Furthermore, heat shock proteins were identified under cold and heat stress, respectively, suggesting these genes participate in reducing cold and heat stress detrimental effect by interacting with TFs or other genes related to abiotic stresses, chlorophyll and photosynthesis, osmoprotectants, and phytohormone as well.

Conclusion:

This study not only underlying B. platyphylla’s molecular mechanism in response to temperature stresses but also provides candidate genes involved in response to temperature stresses.

Keywords:
Cold; Heat; Transcriptome; White birch.

HIGHLIGHTS

26 RNA-Seq libraries were evaluated to figure out molecular changes under. Cold and heat stress in wild type Betula platyphylla seedlings. A total of 104 DEGs were identified under both cold and heat stress. MYB66, bZIP7, bHLH96, and HSP21 play crucial role in cold stress. CBF2, bHLH96, and HSP21 play crucial role in heat stress.

Type of treatment	sample ID	Clean reads	Mapped reads	Mapped reads (%)	Type of treatment	sample ID	Clean reads	Mapped reads	Mapped reads (%)
Control	Ck_rep 1	30,910,157	29,700,540	96.09	Control	Ck_rep 2	29,677,699	28,574,852	96.28
6 ^oC	6 hours_rep 1	29,022,648	27,863,919	96.01	35 ^oC	6 hours_rep 1	32,367,458	30,968,005	95.68
	6 hours_rep 2	32,451,187	31,383,313	96.71		6 hours_rep 2	32,219,968	30,834,931	95.70
	24 hours_rep 1	30,235,523	29,207,979	96.60		24 hours_rep 1	30,834,931	28,710,276	93.11
	24 hours_rep 2	34,737,471	33,511,127	96.47		24 hours_rep 2	27,765,502	26,500,489	95.44
	2 days_rep 1	36,519,078	35,227,291	96.46		2 days_rep 1	40,610,883	38,715,051	95.33
	2 days_rep 2	36,125,564	34,861,176	96.50		2 days_rep 2	36,403,430	34,822,347	95.66
	4 days_rep 1	32,805,042	31,665,283	96.53		4 days_rep 1	36,049,499	34,674,643	96.19
	4 days_rep 2	34,804,068	33,748,669	96.97		4 days_rep 2	38,746,095	37,175,076	95.95
	7 days_rep 1	30,657,043	29,646,750	96.70		7 days_rep 1	33,911,684	32,610,018	96.16
	7 days_rep 2	29,797,476	28,688,469	96.28		7 days_rep 2	31,039,463	30,129,266	97.07
	14 days_rep 1	32,328,230	30,467,486	94.24		14 days_rep 1	33,954,506	32,693,960	96.29
	14 days_rep 2	34,515,820	33,225,231	96.26		14 days_rep 2	27,857,536	26,946,673	96.73

Treatment	Up	Down	Total	Up	Down	Total
Treatment	6 ^OC			35 ^°C
ck vs 6 h	36	27	63	31	19	50
ck vs 24 h	43	43	86	66	53	119
ck vs 2 d	38	54	92	21	32	53
ck vs 4 d	51	41	92	34	23	57
ck vs 7 d	90	43	133	38	25	63
ck vs 14 d	127	80	207	50	36	86

Type of stress	Expression	TF gene ID	Log FC							Function
Type of stress	Expression	TF gene ID	Control	6 h	24 h	2 d	4 d	7 d	14 d	Function
Cold	Up	BPChr04G21825	0.00	8.74	10.27	-	-	16.69	-	Serine/threonine-protein phosphatase PP1 isozyme 4, TOPP4
	Down	BPChr08G10784	4.28	-	200.22	-	224.93	479.61	1117.28	Early light-induced protein 1, ELIP1
		BPChr08G16217	6.34	-	-	0.11	-	-	-	AtBZIP7
		BPChr06G13544	16.04	-	-	-	-	-	0.34	MYB66
		BPChr08G02982	31.16	-	-	0.69	0.25	-	-	Heat Shock Protein 21, HSP21
		BPChr06G31071	73.96	0.00	-	0.00	-	-	-	Sedoheptulose-1,7-bisphosphatase
Heat	Up	BPChr02G23413	0.02	4.31	4.15	-	-	-	-	AtCBF2
	Up	BPChr08G02982	31.17	1458.00	3097.18	-	1447.07	1234.67	-	Heat Shock Protein 21, HSP21
	Down	BPChr06G30704	75.84	-	0.00	-	-	-	-	bHLH096
	Down	BPChr06G30940	1.24	0.00	-	-	-	-	-	Plasma Membrane Intrinsic Protein 1;4, PIP1;4

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[1] Corresponding author: chensu@nefu.edu.cn