Plastid phylogenomic insights into the evolution of subfamily Dialioideae (Leguminosae)

doi:10.1016/j.pld.2020.06.008

Plant Diversity ›› 2021, Vol. 43 ›› Issue (01): 27-34.DOI: 10.1016/j.pld.2020.06.008

Plastid phylogenomic insights into the evolution of subfamily Dialioideae (Leguminosae)

Han-Rui Bai^a,b, Oyetola Oyebanji^a,c, Rong Zhang^a, Ting-Shuang Yi^a

a Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China;
b College of Life Science, Yunnan University, Kunming, Yunnan, 650201, China;
c Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650201, China

收稿日期:2020-01-10 修回日期:2020-06-11 出版日期:2021-02-25 发布日期:2021-03-25
通讯作者: Rong Zhang, Ting-Shuang Yi
基金资助:
This study was supported by grants from the Large-scale Scientific Facilities of Chinese Academy of Sciences (No. 2017-LSF-GBOWS-02), the Strategic Priority Research Program of Chinese Academy of Sciences (XDB31010000), the National Natural Science Foundation of China [key international (regional) cooperative research project No. 31720103903]. We are grateful to Jian-Jun Jin, Shu-Dong Zhang and Xiao-Jian Qu for helpful discussions during the data analysis.

Plastid phylogenomic insights into the evolution of subfamily Dialioideae (Leguminosae)

Han-Rui Bai^a,b, Oyetola Oyebanji^a,c, Rong Zhang^a, Ting-Shuang Yi^a

a Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China;
b College of Life Science, Yunnan University, Kunming, Yunnan, 650201, China;
c Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650201, China

Received:2020-01-10 Revised:2020-06-11 Online:2021-02-25 Published:2021-03-25
Contact: Rong Zhang, Ting-Shuang Yi
Supported by:
This study was supported by grants from the Large-scale Scientific Facilities of Chinese Academy of Sciences (No. 2017-LSF-GBOWS-02), the Strategic Priority Research Program of Chinese Academy of Sciences (XDB31010000), the National Natural Science Foundation of China [key international (regional) cooperative research project No. 31720103903]. We are grateful to Jian-Jun Jin, Shu-Dong Zhang and Xiao-Jian Qu for helpful discussions during the data analysis.

摘要/Abstract

摘要： The subfamily Dialioideae (Leguminosae) consists of 17 genera and about 85 species. Previous studies have detected significant plastid genome (plastome) structure variations in legumes, particularly in subfamilies Papilionoideae and Caesalpinioideae. Hence it is important to investigate plastomes from the newly recognized Dialioideae to better understand the plastome variation across the whole family. Here, we used nine plastomes representing nine genera of Dialioideae to explore plastome structural variation and intergeneric relationships in this subfamily. All plastomes of Dialioideae exhibited a typical quadripartite structure, and had relatively conserved structure compared with other legume subfamilies. However, the genome size ranged from 154,124 bp to 165,973 bp and gene numbers ranged from 129 to 132, mainly due to the expansion and contraction of the inverted repeat (IR) regions. The IR of Distemonanthus benthamianus has experienced two separate expansions into the large single copy (LSC) region and the small single copy (SSC) region, and one contraction from SSC. Poeppigia procera has experienced two separate IR expansions into LSC, while Dicorynia paraensis has experienced an IR contraction from LSC. Highly divergent regions or genes (ndhC-trnV^UAC,psbK-trnQ^UUG,rps19-rps3, rpl33-rps18,accD-psaI,trnG^UCC-trnS^GCU,psbI-trnS^GCU,5'rps16-trnQ^UUG and ycf1) were identified as potential molecular markers for further species delimitation and population genetics analysis in legumes. Phylogenetic analysis based on 77 protein-coding sequences fully resolved the intergeneric relationships among nine genera except a moderately supported sister relationship between Petalostylis labicheoides and Labichea lanceolata. Our study reveals new insights into the structural variations of plastomes in subfamily Dialioideae and advances our understanding of the evolutionary trajectories of legume plastomes.

关键词: Dialioideae, Plastome, IR expansion/contraction, Fabaceae, Variation

Abstract: The subfamily Dialioideae (Leguminosae) consists of 17 genera and about 85 species. Previous studies have detected significant plastid genome (plastome) structure variations in legumes, particularly in subfamilies Papilionoideae and Caesalpinioideae. Hence it is important to investigate plastomes from the newly recognized Dialioideae to better understand the plastome variation across the whole family. Here, we used nine plastomes representing nine genera of Dialioideae to explore plastome structural variation and intergeneric relationships in this subfamily. All plastomes of Dialioideae exhibited a typical quadripartite structure, and had relatively conserved structure compared with other legume subfamilies. However, the genome size ranged from 154,124 bp to 165,973 bp and gene numbers ranged from 129 to 132, mainly due to the expansion and contraction of the inverted repeat (IR) regions. The IR of Distemonanthus benthamianus has experienced two separate expansions into the large single copy (LSC) region and the small single copy (SSC) region, and one contraction from SSC. Poeppigia procera has experienced two separate IR expansions into LSC, while Dicorynia paraensis has experienced an IR contraction from LSC. Highly divergent regions or genes (ndhC-trnV^UAC,psbK-trnQ^UUG,rps19-rps3, rpl33-rps18,accD-psaI,trnG^UCC-trnS^GCU,psbI-trnS^GCU,5'rps16-trnQ^UUG and ycf1) were identified as potential molecular markers for further species delimitation and population genetics analysis in legumes. Phylogenetic analysis based on 77 protein-coding sequences fully resolved the intergeneric relationships among nine genera except a moderately supported sister relationship between Petalostylis labicheoides and Labichea lanceolata. Our study reveals new insights into the structural variations of plastomes in subfamily Dialioideae and advances our understanding of the evolutionary trajectories of legume plastomes.

Key words: Dialioideae, Plastome, IR expansion/contraction, Fabaceae, Variation

Han-Rui Bai, Oyetola Oyebanji, Rong Zhang, Ting-Shuang Yi. Plastid phylogenomic insights into the evolution of subfamily Dialioideae (Leguminosae)[J]. Plant Diversity, 2021, 43(01): 27-34.

图/表 5

参考文献 29

[1]	Baeta F, Costa MJ, Cabral H (2009) Changes in the trophic level of Portuguese landings and fish market price variation in the last decades.Fisheries Research, 97, 216-222.
[2]	Branch TA, Watson R, Fulton EA, Jennings S, McGilliard CR, Pablico GT, Daniel Ricard D, Tracey SR (2010) The trophic fingerprint of marine fisheries.Nature, 468, 431-435.
[3]	Chao M (晁敏), Quan WM (全为民), Li CH (李纯厚), Cheng YH (程炎宏) (2005) Changes in trophic level of marine catches in the East China Sea region.Marine Sciences(海洋科学), 29(9), 51-55. (in Chinese with English abstract)
[4]	Cheng JH (程家骅) (2008) Summer Fishing Ban implementa- tion review: the role of Summer Fishing Ban in resource conservation.China Fisheries(中国水产), (8), 17-19. (in Chinese)
[5]	Cheng JS (程济生), Zhu JS (朱金声) (1997) The feeding characteristics and throphic level of main commercial invertebrates in the Yellow Sea.Acta Oceanologica Sinica(海洋学报), 19, 102-108. (in Chinese)
[6]	Deng JY (邓景耀), Jiang WM (姜卫民), Yang JM (杨纪明), Li J (李军) (1997) Species interaction and food web of major predatory species in the Bohai Sea.Journal of Fishery Sciences of China(中国水产科学), 4, 1-7. (in Chinese with English abstract)
[7]	Du JG (杜建国), Chen B (陈彬), Lu ZB (卢振彬), Song PQ (宋普庆), Xu ZC (许章程), Yu WW (俞炜炜), Song XK (宋希坤) (2010) Changes of fish diversity and trophic levels in Quanzhou Bay.Biodiversity Science(生物多样性), 18, 420-427. (in Chinese with English abstract)
[8]	Du JG (杜建国), Liu ZH (刘正华), Yu XG (余兴光), Xu ZC (许章程), Hu WJ (胡文佳), Chen B (陈彬), Ma ZY (马志远), Lin JL (林金兰) (2012) Fish species diversity and trophic level in the Jiulong Estuary. Journal of Tropical Oceanography(热带海洋学报), 31(6), 76-82. (in Chinese with English abstract)
[9]	Edwards M, Richardson AJ (2004) Impact of climate change on marine pelagic phenology and trophic mismatch.Nature, 430, 881-884.
[10]	Huang LM (黄良敏), Zhang YZ (张雅芝), Pan JJ (潘佳佳), Cui YX (崔裕侠), Wu YJ (吴亚娟) (2008) Food web of fish in Xiamen eastern waters.Journal of Oceanography in Taiwan Strait(台湾海峡), 27, 64-73. (in Chinese with English abstract)
[11]	IMBER (2005) Science Plan and Implementation Strategy. IGBP Report No. 52, IGBP Secretariat, Stockholm.
[12]	Li XD (李雪丁), Lu ZB (卢振彬) (2008) The productivity of fishery resources and the maximum sustained yield in Fujian Coastal Water.Journal of Xiamen University (Natural Science)(厦门大学学报 (自然科学版)), 47, 596-601. (in Chinese with English abstract)
[13]	Lu ZB (卢振彬), Huang MZ (黄美珍) (2004) Studies on trophic level and organic carbon contents of main economic nekton in Fujian coastal waters.Journal of Oceanography in Taiwan Strait(台湾海峡), 23, 153-158. (in Chinese with English abstract)
[14]	Milessi AC, Arancibia H, Neira S, Defeo O (2005) The mean trophic level of Uruguayan landings during the period 1990-2001.Fisheries Research, 74, 223-231.
[15]	Pauly D, Christensen V, Dalagaard J, Froese R, Torres F (1998) Fishing down marine food webs.Science, 279, 860-863.
[16]	Pauly D, Christensen V, Guenette S, Tony JP, Sumaila UR, Walters CJ, Watson R, Zeller D (2002) Towards sustainability in world fisheries.Nature, 418, 689-695.
[17]	Pauly D, Hilborn R, Branch TA (2013) Fisheries: does catch reflect abundance?Nature, 494, 303-306.
[18]	Pauly D, Palomares ML, Froese R, Sa-a P, Vakily M, Preikshot D, Wallace S (2001) Fishing down Canadian aquatic food webs.Canadian Journal of Fisheries and Aquatic Sciences, 58, 51-62.
[19]	Pauly D, Watson R (2005) Background and interpretation of the ‘Marine Trophic Index’ as a measure of biodiversity.Philosophical Transactions of the Royal Society, 360, 415-423.
[20]	Perry AL, Low PJ, Ellis JR, Reynolds JD (2005) Climate change and distribution shifts in marine fishes.Science, 308, 1912-1915.
[21]	Powers JE (2010) Fisheries: measuring biodiversity in marine ecosystems.Nature, 468, 385-386.
[22]	Qiu SY (丘书院), Yang SY (杨圣云), Hong GC (洪港船) (1991) Food relationship of the principal pelagic fishes in Minnan-Taiwan Bank Fishing Ground. In: Minnan-Taiwan Bank Fishing Ground Upwelling Ecosystem Study (闽南-台湾浅滩渔场上升流区生态系统研究) (eds Hong HS (洪华生), Qiu SY (丘书院), Ruan WQ (阮五崎), Hong GC (洪港船)). Science Press, Beijing. (in Chinese)
[23]	Secretariat of the Convention on Biological Diversity (2010) Global Biodiversity Outlook 3. Montréal.
[24]	Tang QS, Jin XS, Wang J, Zhuang ZM, Cui Y, Meng TX (2003) Decadal-scale variation of ecosystem productivity and control mechanisms in the Bohai Sea.Fisheries Oceanography, 12, 223-233.
[25]	Wei S (韦晟), Jiang WM (姜卫民) (1992) Study on food web of fishes in the Yellow Sea.Oceanologia et Limnologia Sinica(海洋与湖沼), 23, 182-192. (in Chinese with English abstract)
[26]	Xu HG, Tang XP, Liu JY, Ding H, Wu J, Zhang M, Yang QW, Cai L, Zhao HJ, Liu Y (2009) China’s progress toward the significant reduction of the rate of biodiversity loss.BioScience, 59, 843-852.
[27]	Yang JM (杨纪明) (2001) A study on food and trophic levels of Bohai Sea fish.Modern Fisheries Information(现代渔业信息), 16(10), 10-19. (in Chinese with English abstract)
[28]	Zhang B (张波), Tang QS (唐启升) (2004) Study on trophic level of important resources species at high trophic levels in the Bohai Sea, Yellow Sea and East China Sea.Advances in Marine Science(海洋科学进展), 22, 392-404. (in Chinese with English abstract)
[29]	Zhang QY (张其永), Lin QM (林秋眠), Lin YT (林尤通), Zhang YP (张月平) (1981) Food web of fishes in Minnan-Taiwan Chientan Fishing Ground.Acta Oceanologica Sinica(海洋学报), 3, 275-290. (in Chinese with English abstract)

	年份 Year							文献来源 Reference
	1959	1982- 1983	1985- 1986	1992- 1993	1998- 1999	2000- 2001	2008- 2010	文献来源 Reference
渤海 Bohai Sea	4.06	3.70	-	3.51	3.41	-	-	张波和唐启升, 2004
黄海 Yellow Sea	-	-	3.66	-	-	3.40	-	张波和唐启升, 2004
东海 East China Sea	-	-	-	-	-	3.68	-	张波和唐启升, 2004
闽东 East Fujian	-	-	-	-	3.57	-	-	李雪丁和卢振彬, 2008
闽中 Middle Fujian	-	-	-	-	3.55	-	-	李雪丁和卢振彬, 2008
闽南 South Fujian	-	-	-	-	3.54	-	-	李雪丁和卢振彬, 2008
泉州湾 Quanzhou Bay	-	3.79	3.79	-	3.58	3.58	3.54	杜建国等, 2010
九龙江口 Jiulongjiang Estuary	-	3.82	3.82	-	3.58	3.58	3.55	杜建国等, 2012
全国 China	3.46 (3.65)	3.44 (3.59)	3.32 (3.58)	3.26 (3.51)	3.22 (3.47)	3.23 (3.48)	3.34 (3.53)

	年份 Year							文献来源 Reference
	1959	1982- 1983	1985- 1986	1992- 1993	1998- 1999	2000- 2001	2008- 2010	文献来源 Reference
渤海 Bohai Sea	4.06	3.70	-	3.51	3.41	-	-	张波和唐启升, 2004
黄海 Yellow Sea	-	-	3.66	-	-	3.40	-	张波和唐启升, 2004
东海 East China Sea	-	-	-	-	-	3.68	-	张波和唐启升, 2004
闽东 East Fujian	-	-	-	-	3.57	-	-	李雪丁和卢振彬, 2008
闽中 Middle Fujian	-	-	-	-	3.55	-	-	李雪丁和卢振彬, 2008
闽南 South Fujian	-	-	-	-	3.54	-	-	李雪丁和卢振彬, 2008
泉州湾 Quanzhou Bay	-	3.79	3.79	-	3.58	3.58	3.54	杜建国等, 2010
九龙江口 Jiulongjiang Estuary	-	3.82	3.82	-	3.58	3.58	3.55	杜建国等, 2012
全国 China	3.46 (3.65)	3.44 (3.59)	3.32 (3.58)	3.26 (3.51)	3.22 (3.47)	3.23 (3.48)	3.34 (3.53)

Plastid phylogenomic insights into the evolution of subfamily Dialioideae (Leguminosae)

Plastid phylogenomic insights into the evolution of subfamily Dialioideae (Leguminosae)

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年份 Year	大陆物种数 Specie number in Mainland	台湾物种数 Specie number in Taiwan	香港物种数 Specie number in Hong Kong	澳门物种数 Specie number in Macau	年份 Year	大陆物种数 Specie number in Mainland	台湾物种数 Specie number in Taiwan	香港物种数 Specie number in Hong Kong	澳门物种数 Specie number in Macau
1950	9	31	22	2	1982	18	71	30	4
1951	9	32	22	2	1983	18	73	30	4
1952	9	34	22	2	1984	18	71	30	4
1953	9	34	23	2	1985	18	72	30	4
1954	9	35	24	2	1986	19	74	30	4
1955	9	36	24	2	1987	21	73	31	4
1956	9	44	22	2	1988	21	72	31	4
1957	9	44	24	2	1989	21	91	31	4
1958	9	58	22	2	1990	27	92	31	4
1959	9	58	22	2	1991	27	90	32	4
1960	9	57	22	2	1992	27	91	32	4
1961	9	59	22	2	1993	27	93	30	4
1962	9	61	23	2	1994	27	93	30	4
1963	9	60	23	2	1995	31	92	31	4
1964	9	61	25	2	1996	30	90	30	4
1965	9	60	24	2	1997	30	90	30	4
1966	9	63	24	2	1998	31	91	30	4
1967	9	65	27	2	1999	31	89	29	4
1968	9	63	29	2	2000	31	88	29	4
1969	9	65	29	2	2001	36	89	29	4
1970	14	69	29	2	2002	37	85	29	4
1971	13	73	29	2	2003	49	90	29	4
1972	14	71	29	2	2004	43	84	29	4
1973	11	71	29	4	2005	43	83	29	4
1974	10	70	29	4	2006	43	85	29	4
1975	10	71	29	4	2007	43	84	29	4
1976	12	70	29	4	2008	42	84	29	4
1977	13	71	30	4	2009	42	85	29	4
1978	17	73	30	4	2010	41	81	29	4
1979	18	72	30	4	2011	41	85	29	4
1980	18	75	30	4	总计	51	101	32	4
1981	18	73	30	4	Total

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