Plastome phylogenomics of the East Asian endemic genus Dobinea

doi:10.1016/j.pld.2020.05.002

Abstract

Abstract: Dobinea is a dioecious genus endemic to East Asia that consists of two extant species: Dobinea delavayi and Dobinea vulgaris. Although the genus is morphologically distinct, its phylogenetic position remains controversial. In this study, we investigated the phylogenetic relationships between Dobinea and related taxa by sequencing the whole plastome DNA sequences for both extant species of Dobinea and comparing them to published plastomes within Sapindales. The complete plastomes of D. vulgaris and D. delavayi were 160,683 and 160, 154 base pairs (bp) in length, including a pair of inverted repeat regions (IRs, 26,889 and 26,759 bp) divided by the large single-copy region (LSC, 87,962 and 87,555 bp) and small single-copy region (SSC, 18,943 and 19,081 bp), and identically encoded 113 unique genes (79 protein-coding genes, 30 tRNAs, and 4 rRNA genes). Plastid phylogenomic analyses showed that Dobinea was a well-supported monophyletic unit and sister to the clade including tribes Anacardieae and Rhoideae, which suggests that Dobinea is a member of Anacardiaceae. In addition, molecular dating inferred D. delavayi and D. vulgaris diverged approximately 10.76 Ma, suggesting the divergence between these two species may have been driven by the intensification of the Asian summer monsoon and the establishment of distinct monsoon regimes in East Asia.

Key words: Neo-endemism, Divergence, Dobinea delavayi, Dobinea vulgaris, Dobineeae, Anacardiaceae

Changkun Liu, Jin Yang, Lei Jin, Shuying Wang, Zhenyan Yang, Yunheng Ji. Plastome phylogenomics of the East Asian endemic genus Dobinea[J]. Plant Diversity, 2021, 43(01): 35-42.

Figures/Tables 5

References 21

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Year	古北型 Palearctic	东洋型 Oriental	不易归类 Widespread	全北型 Holearctic	中亚型 Central Asian	高地型 Highland	东北型 Northeast China	东北-华北型 Northeast-north China	合计 Total
1988	18(23.68%)	2(2.63%)	26(34.21%)	12(15.79%)	10(13.16%)	5(6.58%)	2(2.63%)	1(1.32%)	76
2002	16(20.51%)	4(5.13%)	28(35.90%)	12(15.38%)	10(12.82%)	3(3.85%)	3(3.85%)	1(1.28%)	78
2012	18(21.43%)	5(5.95%)	29(34.52%)	12(14.29%)	12(14.29%)	5(5.95%)	2(2.38%)	1(1.19%)	84

Year	古北型 Palearctic	东洋型 Oriental	不易归类 Widespread	全北型 Holearctic	中亚型 Central Asian	高地型 Highland	东北型 Northeast China	东北-华北型 Northeast-north China	合计 Total
1988	18(23.68%)	2(2.63%)	26(34.21%)	12(15.79%)	10(13.16%)	5(6.58%)	2(2.63%)	1(1.32%)	76
2002	16(20.51%)	4(5.13%)	28(35.90%)	12(15.38%)	10(12.82%)	3(3.85%)	3(3.85%)	1(1.28%)	78
2012	18(21.43%)	5(5.95%)	29(34.52%)	12(14.29%)	12(14.29%)	5(5.95%)	2(2.38%)	1(1.19%)	84

物种 Species	第一次科考 The first investigation (1,195 capture)	第三次科考 The third investigation (1,004 capture)
子午沙鼠 Meriones meridianus	2.59 (31)	2.69 (27)
柽柳沙鼠 M. tamariscinus	0.17 (2)	0.7 (7)
灰仓鼠 Cricetulus migratorius	0.75 (9)	0.6 (6)
三趾跳鼠 Dipus sagitta	4.69 (56)	2.29 (23)
长耳跳鼠 Euchoreutes noso	1.67 (20)	1.1 (11)
五趾跳鼠 Allactaga sibirica	2.51 (30)	1.2 (12)
戈壁五趾跳鼠 A. bullata	+	0.1 (1)
小五趾跳鼠 A. elater		0.2 (2)
捕获率合计 Total capture rate	12.38 (148)	8.86 (89)
Shannon-Wiener diversity index (H)	1.5178	1.7577
均匀度指数 Evenness index (E)	0.8471	0.8453

物种 Species	第一次科考 The first investigation (1,195 capture)	第三次科考 The third investigation (1,004 capture)
子午沙鼠 Meriones meridianus	2.59 (31)	2.69 (27)
柽柳沙鼠 M. tamariscinus	0.17 (2)	0.7 (7)
灰仓鼠 Cricetulus migratorius	0.75 (9)	0.6 (6)
三趾跳鼠 Dipus sagitta	4.69 (56)	2.29 (23)
长耳跳鼠 Euchoreutes noso	1.67 (20)	1.1 (11)
五趾跳鼠 Allactaga sibirica	2.51 (30)	1.2 (12)
戈壁五趾跳鼠 A. bullata	+	0.1 (1)
小五趾跳鼠 A. elater		0.2 (2)
捕获率合计 Total capture rate	12.38 (148)	8.86 (89)
Shannon-Wiener diversity index (H)	1.5178	1.7577
均匀度指数 Evenness index (E)	0.8471	0.8453