Because the genomes of domestic species (except for chicken) were used as the reference genomes for mapping, and the wild species usually have lower read mapping ratios compared to the domestic species (Additional file 1: Figure S3), it is necessary to determine whether mapping bias caused by genetic differences between the genomes of domestic and wild species would reverse the pattern of decreased expression diversity. To test this, we mapped the reads of rice by using the reference genome of the wild species, O. nivara (GCA_000576065.1), and analysed the gene expression diversity of the wild and cultivated rice. The degree of decreased gene expression diversity of the cultivated species (1.054) compared to the wild species (1.205) was even higher (12.5% decrease, P < 2.2e-16) than that obtained using the genome of Oryza japonica as the reference (5.1% decrease, P < 1.1e-12) (Table 2, Additional file 1: Figure S4), indicating that a lower mapping ratio may underestimate the expression diversity of wild species and the degree of decreased expression diversity when the genome of domestic species is used. In addition, we also observed significantly lower expression diversity in the domestic chicken when using the genome of wild chicken (Gallus gallus) as the reference genome (Fig. 1a, Table 2). These results suggest that mapping ratio differences caused by reference genome difference between the domestic and wild species do not change the observed result.
Towards eight sets, the brand new candidate countries you to undergone choosy sweeps throughout the domestication was in fact in the past advertised [fourteen, 18, 28, 30,32,33,34,35]. We put the family genes located in the applicant choosy sweep regions on applicant selected gene put (CSGS) for each tamed types and also the almost every other family genes maybe not located in these types of choosy brush places was in fact placed in the new low-candidate selected gene set (non-CSGS).
For the CSGS, pair-wise comparisons between domestic and wild species of dog, silkworm, rice, cotton, landrace soybean and maize (ear) revealed significantly (P < 0
To have grain, a proper-recognized earlier investigation identified ten,674 applicant chosen genes, hence illustrated % of your own whole genome genetics . Possibly due to the all the way down sequencing depth put during the time, brand new selective sweeps recognized in rice for the reason that investigation may not become exact because part of applicant chosen genes is much huge when you look at the rice compared to one other kinds: 7.3% during the sunflower , 4.05% in the maize [thirteen, 34] and you may six.67% for the soybean (Dining table 2). Hence, i put 144 trials (Additional file dos: Table S9) including 42 wild rice accessions in the NCBI (PRJEB2829) and you will 102 developed accessions from the 3000 Rice Genomes Venture so you can reanalyse new choosy sweeps during the rice. Eventually, i recognized 95 selective brush nations having fun with good.
We further investigated the alterations from gene phrase assortment from the applicant forcibly chose genes
probability strategy (XP-CLR). These types of countries consisted of just 6892 candidate picked genetics and you will illustrated eight.57% of your entire-genome family genes (Dining table 2, A lot more file dos: Desk S10). Multiple well-recognized tamed genetics was contained in the this new candidate picked gene number, along with An enthusiastic-step one (awn advancement), An-2 (LOGL6, awn length controls), GAD1 (cereals invention), OsC1 (leaf sheath the colour and you can apiculus the colour), OsLG1 (panicle structures), sh4 (vegetables smashing), and you will PROG1 (PROSTRATE Development step 1, tiller perspective and you may number of tillers), indicating one to rice candidate selected countries have been well-identified within our the latest abilities (A lot more file step one: Contour S5). Therefore, fewer than 8% of your entire-genome genetics was basically affected during the https://hookupfornight.com/couples-seeking-men/ domestication in different affiliate domestic varieties (Dining table 2).
After obtaining the CSGS (Table 2) for each domestic species, we calculated the expression diversity for the CSGS and non-CSGS. 05) lower expression diversity in the domestic species. In addition, both subgenomes of cotton, namely, the At (17.2% decrease) and Dt (21.9% decrease) subgenomes (Table 2, Additional file 1: Figure S1b, Additional file 2: Table S11), had significantly lower expression diversity in the domestic species for the CSGS. Unlike in the WGGS, the landraces of soybean showed significantly decreased expression diversity in the candidate domesticated gene set (5.6% decrease, P = 0.046) (Fig. 1b, Table 2). Except the gene expression diversity of CSGS for chicken (P = 0.071), the leaf (P = 0.054) and stem (P = 0.087) of maize, and the improved soybean (P < 0.1146) were not significant, all the domestic species showed various degrees of decreased expression diversity in the CSGS, and the percentages reduction in expression for dog, silkworm, chicken, rice, landrace and improved soybean, cotton, and the ear, leaf and stem of maize were 16.1, 34.0, 19.1, 7.0, 5.6, 4.3, 20.6, 13.0, 5.6 and 4.4%, respectively (Table 2).