| Naemorhedus(Mammalia: Artiodactyla: Bovidae: Caprinae)includes three species and six subspecies,among which N.goral is widely distributed in China as well as in other countries e.g.South Asia,Central Asia and Russia.Naemorhedus goral is an endangered species and regarded as a national Class II key protected wild animal.In this study,we sequenced the complete mitochondrial genome(mitogenome)of Naemorhedus goral from North China using High-throughput sequencing method.We downloaded the Caprinae mitochondrial genomes from Genbank and constructed the phylogenetic trees to confirm the classification position of N.goral.The main results are as follows:1)The complete mitogenome of Naemorhedus goral was totally16,559 bp in length,and consisted of a major non-coding control region(D-loop region),two ribosomal RNAs(12S and 16 S rRNA)genes,13protein-coding genes(ND1,ND2,ND3,ND4,ND4 L,ND5,and ND6;COX1,COX2,and COX3;ATP 6 and ATP 8;and Cytb),and 22 transfer RNA genes.2)The base composition was 33.6% A,27.2% T,26.0% C,and 13.2%G,respectively,and the content of A+T in mtDNA is higher than that of G+C.Of these genes,ATP 6 and eight tRNAs(tRNA-Gln,tRNA-Ala,tRNA-Asn,tRNA-Cys,tRNA-Tyr,tRNA-Ser,tRNA-Glu,and tRNA-Thr)were encoded in the L-strand,while the others were encoded in the H-strand.3)Ten of the 13 protein-coding genes use ATG as the start codon,while ND5 and ND6 starting with ATT and TTA,respectively.Six of 13protein-coding genes use TAA as stop codons.The Cytb stop with AGA,ND6 ends with CAT,and five(ND1,ND2,COX3,ND3 and ND4)use T as an incomplete stop codon,which were presumably completed as TAA by post-transcriptional polyadenylation.4)There were 22 tRNA genes in the mitochondrial genome of the goat.Their lengths ranged from 60bp(tRNA-Ala)to 75bp(tRNA-Leu),and theywere distributed in protein-coding genes and rRNA genes.12 S rRNA and16 S rRNA were 957 bp and 1,570 bp in length,respectively,and were located between tRNA-Phe and tRNA-Leu and separated by tRNA-Val,as is the case in other Caprinae.16 S rRNA in the Naemorhedus goral was 4 bp longer than the N.griseus,but 12 S rRNA was the same in length and location in the N.griseus.5)We downloaded the 13 protein coding gene sequences of Caprinae with Alcelaphinae and Hippotraginae as outgroups from GenBank and aligned by MAFFT implemented in Geneious v10.0.5,and separately reconstructed phylogenetic relationships in PAUP*4.0b10 under the GTR-GAMMA model and with 1000 bootstrap replicates.The phylogenetic relationship indicated that Caprinae species grouped into two big clades and Naemorhedus is a monophy-letic group with high bootstrap values.N.goral from North China was grouped into N.griseus,and then clustered with N.goral from Himalayan with well support.Such information is very crucial not only to develop and screen Caprinae DNA barcodes,but also to thoroughly understand of the evolutionary history and rare genetic resource conservation of Caprinae.However,more samples ought to be added to further clarify the population variation of the two species N.goral and N.griseus.Rhus punjabensis var.sinica(Anacardiaceae)is widely distributed in China.and has high economic values mostly used in medicine and planting.It has a certain fire-retardant and anti-inflammatory effect and the effect of a single use is very good.The Rhus Gall Aphids(Hemiptera: Aphididae),parasitize on Rhus punjabensis var.sinica,which are important medical and industrial materials.We sequenced the psb A and trnL gene of the chloroplast DNA of R.punjabensis var.sinica populations from 101 individuals presenting six locations to analyze the genetic diversity and genetic structure.The main results are as following:1)We obtained R.punjabensis var.sinica cp DNA sequences 1449 bp in length with psb A 581 bp and trn L 868 bp.The content of T,C,A,G of psb A,trn L and combined sequences are 37.9%?11.1%?37.3%?13.7%;28.0%?19.1%?35.0%?17.9% and 31.9%?15.9%?36.0%?16.2%;The content of A+T in cp DNA is higher than that of G+C,The trn L-psb A?trn L-F sequence and combined sequences former included 35?10?45 variable sites and 546?858?1404 conserved sites(93.3%).2)we obtained the trnL-psbA sequence,the trnL-F sequence,psbA and trn L Combined sequences.respectively.The haplotype diversitywere 0.717± 0.034,0.435± 0.059,0.783± 0.038.And the nucleotide diversity were0.00460±0.00100,0.00087±0.00014,0.00340±0.00049.The data analysis showed that R.punjabensis var.sinica haplotype diversity and the nucleotide diversity is high.3)We have the trnL-psbA sequence of 15 haplotypes(Hap)from R.punjabensis var.sinica And the haplotype Hap1 was the most widely distributed and shared by six populations;Hap8 and Hap11 were distributed in two regions.The 9 haplotypes were obtained from the trn L-F sequence sequence analysis,of which only one haplotype(Hap1)was shared by all populations,and the remaining haplotypes all distributed one population.The23 haplotypes were obtained from the sequences of psb A and trn L Combined sequences from chloroplasts of R.punjabensis var.sinica,of which only one haplotype(Hap1)was shared by all populations,and haplotype(Hap8)distributed two populations including Hubei Wufeng and Sichuan Chenggu.4)Analysis of molecular variance(AMOVA)of R.punjabensis var.sinica showed that the genetic variation within populations was much high in the cp DNA trn L-F sequence,while the cp DNA trn L and psb A combined sequences and cp DNA trn H-psb A sequence among populations were greater than within populations,and the FST values were 0.59643 and 0.56511.5)The TCS network based on a single gene and a combination of genes showed that different haplotypes of R.punjabensis var.sinica groups clustered into nodes with no obvious clusters.It was analyzed that there was no new species in R.punjabensis var.sinica groups.Therefore,species identification can be performed using a DNA sequence molecular marker method.6)Based on Tajima's D value and distribution of bifurcation point,we could draw a conclusion that population expansion event was happened in R.punjabensis var.sinica. |
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