Genome-wide identification of full-length long-terminal repeat retrotransposons and identification of interrupted genes in Cleistogenes songorica

doi:10.11686/cyxb2020219

Abstract

Abstract:

Long-terminal repeat retrotransposons （LTR-RTs） are mobile genetic factors that are an important component of， and are widely distributed across， the plant genome. The genome of Cleistogenes songorica is 543 M in size. In total， 299079 LTR-RTs have been identified in C. songoria， accounting for 26.54% of the total genome. The aim of this study was to identify full-length LTR-RTs in the C. songorica genome and determine when they arose and which genes they interrupt. Based on the whole genome sequence of C. songorica， 845 potential full-length LTR-RTs were identified， of which 410 belong to the Gypsy superfamily and 435 belong to the Copia superfamily. These sequences were subjected to phylogenetic and insertion time analyses. The results of those analyses indicated that many full-length LTR-RTs have been transposed within the last 4 million years. The range of insertion time was relatively short， and the peak period of LTR-RTs insertion was between 1 and 1.5 million years ago. We identified 183 genes that have been interrupted by full-length LTR-RTs in C. songorica， and 145 of them were annotated with Gene Ontology functions. We analyzed the transcript levels of the interrupted genes under different drought stress treatments. Identification of the dynamics of retrotransposons is helpful for understanding the complexities of C. songorica evolution， and lays the foundation for further research and analysis of full-length LTR-RTs in C. songorica.

Key words: Cleistogenes songorica, full length LTR retrotransposons, insertion time, interrupted genes, genome

Yi-meng WANG, Tian-tian MA, Zi-feng OUYANG, Ji-yu ZHANG. Genome-wide identification of full-length long-terminal repeat retrotransposons and identification of interrupted genes in Cleistogenes songorica[J]. Acta Prataculturae Sinica, 2021, 30(5): 121-133.

Figures/Tables 11

References 45

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超家族 Superfamily	Llorens等^[25]定义的进化枝Clades defined by Llorens et al	参考全长LTR-RTs序列 Reference full-length LTR-RTs	宿主有机体 Host organism	无芒隐子草中支系成员数量Number of family members in C. songorica
Copia	Sire	Endovir1 1	拟南芥Arabidopsis thaliana	35
		SIRE1 4	大豆Glycine max
		Opie 2	水稻Oryza sativa
		TSI 9	小米Setaria italica
		ToRTL 1	番茄Solanum lycopersicum
	Oryco	Araco	拟南芥A. thaliana	138
		Vitico1 1	葡萄Vitis vitivinifera
		Vitico1 2	葡萄V. vitivinifera
	Retrofit	Koala	野生稻Oryza australiensis	83
		Retrofit	长雄野生稻Oryza longistaminata
		Hopscotch	水稻O. sativa
	Tork	Sto 4	玉米Zea mays	75
		Tnt 1	烟草Nicotiana tabacum
		V 12	葡萄V. vitivinifera
		Batata	红薯Ipomoea batatas
		Tto1	烟草N. tabacum
		RTvr 2	绿豆Vigna radiata
		Tork 4	番茄S. lycopersicum
Gypsy	Athila	Cyclops-2	豌豆Pisum sativum	1
		Calypso	大豆G. max
		Bagy 2	大麦Hordeum vulgare
		Athila 4-1	拟南芥A. thaliana
		Diapsora	大豆G. max
	Tat	Tat 4-1	拟南芥A. thaliana	182
		Tf t2	拟南芥A. thaliana
		RetroSor 1	高粱Sorghum bicolor
		Cinful 1	玉米Z. mays
		RIRE 2	水稻O. sativa
		Ogre	豌豆P. sativum
	Reina	Reina	玉米Z. mays	63
		Gloin	拟南芥A. thaliana
		Ifg 7	辐射松Pinus radiata
		Gimli	拟南芥A. thaliana
	CRM	Cereba	大麦H. vulgare	47
		CRM	玉米Z. mays
		Beetle 1	甜菜Beta vulgaris
	Galadriel	Monkey	芭蕉Musabasjoo	0
		Galadriel	番茄S. lycopersicum
		Tntom 1	油菜Nicotiana tomentosiformis
	Del/Tekay	Tma	拟南芥A. thaliana	10
		Legolas	拟南芥A. thaliana
		Bagy 1	大麦H. vulgare
		Retrosat 2	水稻O. sativa
		Peabody	豌豆P. sativum
		Del	百合Lilium henryi

超家族 Superfamily	Llorens等^[25]定义的进化枝Clades defined by Llorens et al	参考全长LTR-RTs序列 Reference full-length LTR-RTs	宿主有机体 Host organism	无芒隐子草中支系成员数量Number of family members in C. songorica
Copia	Sire	Endovir1 1	拟南芥Arabidopsis thaliana	35
		SIRE1 4	大豆Glycine max
		Opie 2	水稻Oryza sativa
		TSI 9	小米Setaria italica
		ToRTL 1	番茄Solanum lycopersicum
	Oryco	Araco	拟南芥A. thaliana	138
		Vitico1 1	葡萄Vitis vitivinifera
		Vitico1 2	葡萄V. vitivinifera
	Retrofit	Koala	野生稻Oryza australiensis	83
		Retrofit	长雄野生稻Oryza longistaminata
		Hopscotch	水稻O. sativa
	Tork	Sto 4	玉米Zea mays	75
		Tnt 1	烟草Nicotiana tabacum
		V 12	葡萄V. vitivinifera
		Batata	红薯Ipomoea batatas
		Tto1	烟草N. tabacum
		RTvr 2	绿豆Vigna radiata
		Tork 4	番茄S. lycopersicum
Gypsy	Athila	Cyclops-2	豌豆Pisum sativum	1
		Calypso	大豆G. max
		Bagy 2	大麦Hordeum vulgare
		Athila 4-1	拟南芥A. thaliana
		Diapsora	大豆G. max
	Tat	Tat 4-1	拟南芥A. thaliana	182
		Tf t2	拟南芥A. thaliana
		RetroSor 1	高粱Sorghum bicolor
		Cinful 1	玉米Z. mays
		RIRE 2	水稻O. sativa
		Ogre	豌豆P. sativum
	Reina	Reina	玉米Z. mays	63
		Gloin	拟南芥A. thaliana
		Ifg 7	辐射松Pinus radiata
		Gimli	拟南芥A. thaliana
	CRM	Cereba	大麦H. vulgare	47
		CRM	玉米Z. mays
		Beetle 1	甜菜Beta vulgaris
	Galadriel	Monkey	芭蕉Musabasjoo	0
		Galadriel	番茄S. lycopersicum
		Tntom 1	油菜Nicotiana tomentosiformis
	Del/Tekay	Tma	拟南芥A. thaliana	10
		Legolas	拟南芥A. thaliana
		Bagy 1	大麦H. vulgare
		Retrosat 2	水稻O. sativa
		Peabody	豌豆P. sativum
		Del	百合Lilium henryi

染色 Chromosome	全长LTR-RTs数 Number of full-length LTR retrotransposons (Copia; Gypsy)	Copia∶Gypsy比率 Ratio of Copia∶Gypsy	每千万碱基全长LTR-RTs密度 Density of LTR-RTs per 10 million base length (Copia/Gypsy)	染色体大小 Chromosome size (bp)
Chr1	53 (26; 27)	0.96	14.43 (7.08/7.35)	36730093
Chr2	54 (26; 28)	0.93	15.37 (7.40/7.97)	35137460
Chr3	52 (21; 31)	0.68	15.24 (6.15/9.08)	34124666
Chr4	53 (27; 26)	1.04	16.84 (8.58/8.26)	31471377
Chr5	53 (24; 29)	0.83	16.71 (7.56/9.14)	31725061
Chr6	48 (29; 19)	1.53	15.26 (9.22/2.86)	31461567
Chr7	64 (38; 26)	1.46	20.56 (12.21/8.35)	31124980
Chr8	42 (30; 12)	2.50	13.91 (9.94/3.98)	30186489
Chr9	41 (21; 20)	1.05	15.74 (8.06/7.68)	26050788
Chr10	40 (26; 14)	1.86	15.14 (9.84/5.30)	26425489
Chr11	39 (17; 22)	0.77	15.39 (6.71/8.68)	25340727
Chr12	25 (12; 13)	0.92	12.03 (5.78/6.26)	20776520
Chr13	29 (15; 14)	1.07	13.44 (6.95/6.49)	21572208
Chr14	31 (20; 11)	1.82	14.64 (9.45/5.20)	21171528
Chr15	29 (12; 17)	0.71	14.31 (5.92/8.39)	20269367
Chr16	28 (11; 17)	0.65	14.50 (5.70/8.81)	19304776
Chr17	31 (14; 17)	0.82	16.47 (7.44/9.03)	18816966
Chr18	33 (20; 13)	1.54	17.00 (10.30/6.70)	19417082
Chr19	29 (12; 17)	0.71	17.39 (7.20/10.19)	16677740
Chr20	20 (12; 8)	1.50	12.16 (7.29/4.86)	16453899

染色 Chromosome	全长LTR-RTs数 Number of full-length LTR retrotransposons (Copia; Gypsy)	Copia∶Gypsy比率 Ratio of Copia∶Gypsy	每千万碱基全长LTR-RTs密度 Density of LTR-RTs per 10 million base length (Copia/Gypsy)	染色体大小 Chromosome size (bp)
Chr1	53 (26; 27)	0.96	14.43 (7.08/7.35)	36730093
Chr2	54 (26; 28)	0.93	15.37 (7.40/7.97)	35137460
Chr3	52 (21; 31)	0.68	15.24 (6.15/9.08)	34124666
Chr4	53 (27; 26)	1.04	16.84 (8.58/8.26)	31471377
Chr5	53 (24; 29)	0.83	16.71 (7.56/9.14)	31725061
Chr6	48 (29; 19)	1.53	15.26 (9.22/2.86)	31461567
Chr7	64 (38; 26)	1.46	20.56 (12.21/8.35)	31124980
Chr8	42 (30; 12)	2.50	13.91 (9.94/3.98)	30186489
Chr9	41 (21; 20)	1.05	15.74 (8.06/7.68)	26050788
Chr10	40 (26; 14)	1.86	15.14 (9.84/5.30)	26425489
Chr11	39 (17; 22)	0.77	15.39 (6.71/8.68)	25340727
Chr12	25 (12; 13)	0.92	12.03 (5.78/6.26)	20776520
Chr13	29 (15; 14)	1.07	13.44 (6.95/6.49)	21572208
Chr14	31 (20; 11)	1.82	14.64 (9.45/5.20)	21171528
Chr15	29 (12; 17)	0.71	14.31 (5.92/8.39)	20269367
Chr16	28 (11; 17)	0.65	14.50 (5.70/8.81)	19304776
Chr17	31 (14; 17)	0.82	16.47 (7.44/9.03)	18816966
Chr18	33 (20; 13)	1.54	17.00 (10.30/6.70)	19417082
Chr19	29 (12; 17)	0.71	17.39 (7.20/10.19)	16677740
Chr20	20 (12; 8)	1.50	12.16 (7.29/4.86)	16453899

插入时间 Insertion time (Million years)	绝对频率（相对频率） Absolute frequency (relative frequency)
	Copia 超家族Superfamily					Gypsy超家族Superfamily
	Retrofit	Tork	Sire	Oryco	No cluster	Tat	Reina	CRM	Del	No cluster
0~0.5	11 (0.13)	1 (0.01)	1 (0.03)	17 (0.12)	24 (0.23)*	4 (0.02)	10 (0.16)	11 (0.23)*	1 (0.10)	37 (0.35)*
0.5~1.0	17 (0.20)*	6 (0.08)	6 (0.17)	24 (0.17)	16 (0.25)*	16 (0.09)	19 (0.30)*	10 (0.21)*	1 (0.10)	10 (0.10)
1.0~1.5	24 (0.29)*	8 (0.11)	5 (0.14)	36 (0.26)*	25 (0.24)*	36 (0.20)*	17 (0.27)*	10 (0.21)*	0 (0.00)	15 (0.14)
1.5~2.0	16 (0.19)	7 (0.09)	9 (0.26)*	30 (0.22)*	13 (0.13)	31 (0.17)	9 (0.14)	4 (0.09)	2 (0.20)*	11 (0.10)
2.0~2.5	9 (0.11)	14 (0.19)	7 (0.20)*	21 (0.15)	7 (0.07)	28 (0.15)	1 (0.02)	8 (0.17)	2 (0.20)*	12 (0.11)
2.5~3.0	3 (0.04)	13 (0.18)	3 (0.09)	5 (0.04)	6 (0.06)	24 (0.13)	2 (0.03)	2 (0.04)	1 (0.10)	8 (0.08)
3.5~4.0	0 (0.00)	5 (0.07)	1 (0.03)	1 (0.01)	1 (0.01)	2 (0.01)	0 (0.00)	1 (0.02)	1 (0.10)	5 (0.05)
4.0~4.5	4 (0.05)	8 (0.11)	3 (0.09)	3 (0.02)	1 (0.01)	24 (0.13)	3 (0.05)	0 (0.00)	2 (0.20)*	5 (0.05)
4.5~5.0	0 (0.00)	0 (0.00)	0 (0.00)	1 (0.01)	0 (0.00)	2 (0.01)	1 (0.02)	0 (0.00)	0 (0.00)	1 (0.01)
5.0~5.5	0 (0.00)	4 (0.05)	0 (0.00)	0 (0.00)	1 (0.01)	1 (0.01)	1 (0.02)	1 (0.02)	0 (0.00)	0 (0.00)
5.5~6.0	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)
6.0~6.5	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)
6.5~7.0	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)
7.0~7.5	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)
7.5~8.0	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)
3.0~3.5	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	0 (0.00)	1 (0.01)