Table 1.

List of taxa sampled in this study, with voucher, Illumina reads and GenBank accessions; species names that are underlined represent those species selected for PhyloNet analysis

Taxon	Voucher specimen	Sources	No. of reads (trimmed)	SRA number	Plastid genome
Stewartieae
Stewartia calcicola	YXQ090	Yunnan, China	76 314 960	SRR14596892	KY406783
Stewartia cordifolia	YXQ144	Guangxi, China	101 158 084	SRR14596891	KY406775
Stewartia crassifolia	YXQ171	Hunan, China	88 878 696	SRR14596880	KY406766
Stewartia malacodendron	FLAS 260361	Alabama, USA	1 798 360 616	SRR14596869	KY406773
Stewartia ovata	18847*A	The Arnold Arboretum	100 544 128	SRR14596858	KY406782
Stewartia pseudocamellia	MO-6587810	Missouri Botanical Garden	83 044 916	SRR14596847	KY406786
Stewartia pteropetiolata	YXQ038	Yunnan, China	124 092 532	SRR14596838	KY406770
Stewartia rostrata	YXQ15072003	Jiangxi, China	91 741 812	SRR14596837	KY406789
Stewartia rubiginosa	YXQ189	Hunan, China	91 059 484	SRR14596836	KY406777
Stewartia sinensis	YXQ15072001	Jiangxi, China	91 325 600	SRR14596835	KY406748
Gordonieae
Franklinia alatamaha	MO-6587811	Missouri Botanical Garden	101 387 448	SRR14596890	KY406774
Gordonia brenesii	N. Zamora 7196	Guanacaste, Costa Rica	104 462 244	SRR14596889	KY406761
Gordonia lasianthus	JCRA 110687	JC Raulston Arboretum, Raleigh, NC, USA	82 908 172	SRR14596888	KY406790
Schima argentea	YXQ226	Yunnan, China	86 065 752	SRR14596887	–*
Schima brevipedicellata	YXQ072	Yunnan, China	89 409 700	SRR14596886	KY406784
Schima noronhae	YXQ034	Yunnan, China	88 824 452	SRR14596885	KY406787
Schima sericans	YXQ053	Yunnan, China	97 108 488	SRR14596884	KY406779
Schima superba	YXQ142	Guangxi, China	91 704 880	SRR14596883	KY406788
Schima wallichii	YXQ001	Yunnan, China	89 876 764	SRR14596882	KY406795
Theeae
Apterosperma oblata	YangSX 5978	Guangdong, China	86 466 584	SRR14596881	–
Camellia amplexifolia	YangSX 5010	Hainan, China	98 672 716	SRR14596879	–
Camellia assimiloides	YangSX 5540	Guangdong, China	98 123 144	SRR14596878	–
Camellia cordifolia	YangSX 5551	Guangdong, China	96 616 940	SRR14596877	–
Camellia cuspidata	YangSX 5118	Hubei, China	78 369 336	SRR14596876	–
Camellia flavida	YangSX 5865	Guangxi, China	92 242 904	SRR14596875	–
Camellia fluviatilis	YangSX 4033	Guangxi, China	68 780 488	SRR14596874	–
Camellia grijsii	YangSX 6064	Guizhou, China	120 959 328	SRR14596873	–
Camellia gymnogyna	YangSX 5953	Guangxi, China	94 768 804	SRR14596872	–
Camellia huana	YangSX 5653	Guizhou, China	111 316 580	SRR14596871	–
Camellia ilicifolia	YangSX 5287	Guizhou, China	95 559 812	SRR14596870	–
Camellia longipedicellata	YangSX 5926	Guangxi, China	90 347 792	SRR14596868	–
Camellia longissima	YangSX 5079	Guangxi, China	99 050 172	SRR14596867	–
Camellia luteoflora	YangSX 6063	Guizhou, China	123 788 308	SRR14596866	–
Camellia pilosperma	YangSX 4714	Guangxi, China	92 105 712	SRR14596865	–
Camellia pitardii var. compressa	YangSX 4576	Hunan, China	76 531 640	SRR14596864	–
Camellia semiserrata	YangSX 5555	Guangdong, China	86 751 660	SRR14596863	–
Camellia sinensisvar. pubilimba	YangSX 5927	Guangxi, China	85 785 132	SRR14596862	–
Camellia szechuanensis	YangSX 5064	Sichuan, China	88 726 296	SRR14596861	–
Camellia tsingpienensis	YangSX 5798	Guangxi, China	90 514 420	SRR14596860	–
Camellia tuberculata	YangSX 5202	Chongqing, China	90 076 900	SRR14596859	–
Laplacea fruticosa	NZ10477	Puntarenas, Costa Rica	1 532 313 620	SRR14596857	–
Polyspora axillaris	YXQ099	Hainan, China	92 917 500	SRR14596856	KY406760
Polyspora chrysandra	YXQ221	Yunnan, China	84 011 964	SRR14596855	–
Polyspora dalgleishiana	BROWP 501	Royal Botanic Garden Edinburgh, UK	83 838 300	SRR14596854	KY406769
Polyspora hainanensis	YXQ097	Hainan, China	97 170 208	SRR14596853	KY406776
Polyspora longicarpa	YangSX 4779	Yunnan, China	89 251 900	SRR14596852	KY406768
Polyspora speciosa	YXQ145	Guangxi, China	96 508 612	SRR14596851	KY406754
Pyrenaria hirta var. cordatula	YXQ169	Guangxi, China	92 426 012	SRR14596850	KY406785
Pyrenaria hirta var. hirta	YangSX 4067	Guangxi, China	100 342 800	SRR14596849	–
Pyrenaria jonquieriana  subsp.  multisepala	YXQ106	Hainan, China	87 583 392	SRR14596848	KY406772
Pyrenaria khasiana	YangSX 5046	Myanmar, Kachin	88 528 812	SRR14596846	KY406756
Pyrenaria menglaensis	YXQ211	Yunnan, China	87 085 244	SRR14596845	KY406747
Pyrenaria microcarpa var. microcarpa	YXQ101	Hainan, China	81 080 788	SRR14596844	KY406764
Pyrenaria oblongicarpa	YXQ216	Yunnan, China	98 658 408	SRR14596843	KY406781
Pyrenaria pingpienensis	YXQ210	Yunnan, China	96 601 500	SRR14596842	–
Pyrenaria shinkoensis	YangSX 5038	Taiwan, China	101 120 720	SRR14596841	–
Pyrenaria spectabilis var. greeniae	YXQ172	Hunan, China	93 451 072	SRR14596840	KY406753
Pyrenaria spectabilis  var.   spectabilis	YXQ155	Guangxi, China	88 012 020	SRR14596839	KY406765
Outgroups
Galax urceolata	Diapensiaceae	–	9 647 946	ERX2099546	–
Eurya acuminatissima	Pentaphylacaceae	–	25 009 135	SRX2786652	–
Ternstroemia gymnanthera	Pentaphylacaceae	–	14 421 549	ERX2099558	–
Sinojackia xylocarpa	Styracaceae	–	10 611 525	ERX2099565	–
Symplocos tinctoria	Symplocaceae	–	10 196 542	ERX2099566	–
Symplocos paniculata	Symplocaceae	–	28 374 406	SRX1601992	–

*A dash represents the plastid genes were extracted from the transcriptome data or no data were available.