Gene genealogies indicates abundant gene conversions and independent evolutionary histories of the mating-type chromosomes in the evolutionary history of Neurospora tetrasperma

Menkis, Audrius; Whittle, Carrie A; Johannesson, Hanna

doi:10.1186/1471-2148-10-234

Table 2 Allele divergence between pairs of single mating-type component strains belonging to nine species of the Neurospora tetrasperma species complex

From: Gene genealogies indicates abundant gene conversions and independent evolutionary histories of the mating-type chromosomes in the evolutionary history of Neurospora tetrasperma

Locus^a	Strain pair^b	L1A-L1a			L2A-L2a			L3A-L3a			L4A-L4a			L5A-L5a			L6A-L6a			L7A-L7a			L8(1)A-L8(1)a			L8(2)A-L8(2)a			L9A-L9a
	Lineage^c	1			2			3			4			5			6			7			8			8			9
	Exon sequences (bp)	d _N	d _S	i^d	d _N	d _S	i^d	d _N	d _S	i^d	d _N	d _S	i^d	d _N	d _S	i^d	d _N	d _S	i^d	d _N	d _S	i^d	d _N	d _S	i^d	d _N	d _S	i^d	d _N	d _S	i^d
ro-10	590	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
nit-2	3293	0	0	0	0	0	0	0	0	0	0	0.001	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.002	0	0
krev-1	521	0	0.008	11	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.025	0
sod-1	465	0	0.017	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.009	0
mus-42	1680	0	0.003	-	0	0	-	0	0	-	0	0	-	0	0	-	0.001	0.018	-	0	0	-	0	0	-	0	0	-	0.006	0.060	-
rid	2560	0	0.005	-	0.001	0.004	-	0	0	-	0.010	0.033	-	0.001	0	-	0	0	-	0.001	0	-	0	0	-	0.001	0	-	0.031	0.147	-
leu-4	1863	0	0	0	0.002	0.028	9	0	0.028	3	0.001	0.007	5	0.001	0.028	9	0.001	0.028	10	0	0.030	7	0	0.014	4	0	0.014	4	0.004	0.059	8
cys-5	883	0	0	-	0	0.024	-	0.005	0.024	-	0.002	0.034	-	0	0	-	0	0	-	0.002	0.029	-	0.003	0.015	-	0.003	0.020	-	0.003	0.070	-
ser-3	922	0.004	0.025	-	0	0	-	0	0	-	0.002	0.004	-	0.007	0.047	-	0.007	0.047	-	0.002	0.004	-	0	0	-	0.002	0	-	0.006	0.074	-
tef-1	476	0	0	3	0	0.038	18	0	0.048	17	0	0.019	23	0	0.019	16	0	0.029	16	0	0.009	13	0	0.019	19	0	0.019	20	0	0.048	23
un-3	1924	0.001	0.031	-	0.002	0.048	-	0.002	0.036	-	0.002	0.028	-	0.002	0.048	-	0.003	0.048	-	0	0.048	-	0.001	0.019	-	0.001	0.019	-	0.002	0.045	-
mat
upr-1	2888	0.017	0.053	-	0.021	0.057	-	0.016	0.065	-	0.016	0.048	-	0.021	0.055	-	0.021	0.055	-	0.015	0.054	-	0.004	0.012	-	0.004	0.012	-	0.031	0.079	-
erg-8	1429	0	0.037	3	0.005	0.063	6	0	0.069	4	0.001	0.066	4	0.004	0.063	6	0.003	0.059	6	0.001	0.046	5	0.001	0.037	3	0.001	0.037	3	0.003	0.076	8
arg-1	1119	0	0.008	10	0.001	0.043	13	0	0	0	0	0.043	11	0.001	0.051	13	0.001	0.047	13	0	0.031	8	0	0.019	10	0	0.019	10	0	0.051	19
eth-1	866	0.005	0.005	3	0.002	0.029	5	0.003	0.029	3	0.002	0.034	3	0.002	0.029	5	0.002	0.029	5	0	0.034	4	0.002	0.024	2	0.002	0.024	2	0.002	0.054	5
centromere
lys-4	1055	0.001	0.049	23	0.004	0.053	30	0.005	0.057	9	0	0	0	0.004	0.061	17	0.004	0.061	17	0.006	0.038	7	0.004	0.024	13	0.020	0.020	0	0.006	0.076	15
cys-9	907	0	0.047	7	0	0.082	8	0	0.037	7	0	0.042	6	0	0.082	8	0	0.082	8	0.002	0.023	3	0	0.037	5	0	0.037	9	0	0.057	14
ad-9	609	0.004	0.035	2	0.002	0.072	1	0.002	0.057	5	0.004	0.064	3	0.022	0.072	1	0.002	0.072	1	0.007	0.072	8	0	0.007	0	0	0.007	0	0.004	0.049	3
al-1	1637	0.002	0.032	1	0.004	0.073	17	0.002	0.065	18	0.001	0.029	12	0.004	0.076	17	0.005	0.073	17	0.002	0.073	1	0.005	0.053	15	0.005	0.051	15	0.004	0.054	5
lys-3	3324	0	0.001	0	0.001	0.062	0	0	0	0	0	0	0	0.001	0.062	0	0.001	0.062	0	0.002	0.031	1	0.001	0	0	0.001	0	0	0.002	0.052	5
os-1	1749	0	0	0	0	0	0	0	0.003	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
prd-4	1475	0	0	0	0	0	0	0	0	0	0	0	0	0.001	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
arg-13	999	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
phr	1769	0	0	0	0	0	0	0.001	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

^a Genes are listed from the left to the right flank of the mating-type chromosome according to gene order in N. crassa. The location of the mat-locus and the centromere is indicated.
^b Full strain ID can be found in Table 1. All pairs, except L3A-L3a, originates from one wild-type heterokaryon of N. tetrasperma
^c Genetically and reproductively isolated species described in [5].
^d Number of single nucleotide polymorphisms in intron sequences of the genes

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