Complete Chloroplast Genomes Of Chenopodium Quinoa Strains And Phylogenetic Relationship

Quinoa,belonging to the family Chenopodiaceae and the genus Chenopodium,is an annual dicotyledonous herb that was original at the Andes of South America 5000 years ago.This plant described on plateaus in high-altitude areas,and was one of the main food crops for local people.Quinoa was introduced to our country in 1988,and then was cultivated for small-scale planting and succeeded in Tibet,China.At present,the crop has been planted and producted to extend widely to most places of the north and south of China.However,there are only limited reports on the genetic variation of quinoa from different sources and strains.Here,we used the second-generation high-throughput sequencing technology to sequence,assemble and annotate the chloroplast genomes(cpDNAs)of 13 different quinoa strains in the species Chenopodium quinoa,and analyze the genome characteristics;we downloaded the published cpDNA sequence of quinoa and other Chenopodiaceae species from GenBank;we used bioinformatic methods to compare genomes,construct phylogenetic trees to analyze the genetic variation of different strains and the relationship of different species of Chenopodiaceae.The detailed results are as followings:1.The complete cpDNA sequences of 13 different quinoa strains were obtained with a length of about 152 kb.Among them,the longest cpDNA sequence is 152,194 bp for the sample C.TWH,and there are only 1-4 base differences between the other different strains as 152,086 bp-152,090 bp.The cpDNA of our samples is a double-stranded circular molecule with a four border structure,that is,there are two identical sequences,i.e.,the repeating regions IRa and IRb in opposite directions,between a large single-copy region LSC and a small single-copy region SSC.The length is 152,086-152,194 bp,18,107-18,131 bp and 25,205-25,193 bp,respectively.The SSC area has the smallest difference in length among different strains of quinoa,and the LSC area has the largest difference in length.2.The cpDNAs of 13 Chenopodium samples were annotated with 133 genes,including 88 protein-coding genes,37 r RNA genes and 8 r RNA genes.Among them,the number of different protein coding genes is 80,the number of tRNA genes is 30,and the number of r RNA genes is 4.In addition,there are 19 genes in the IR copy region,including 7 tRNA genes,8 protein coding genes,and all 8 r RNA gene.3.The base composition and codon preference usage of cpDNA sequences of 13 quinoa strains were calculated,and the results were similar in different samples.The average AT content was 62.8%,and the average GC content was 37.2%,which showed high AT and low GC characteristics consistent with other angiosperms.4.The four border regions of cpDNA of different quinoa strains were analyzed by IRscope software,and the results showed that no obvious expansion and contraction occurred.5.The synteny analysis of different quinoa strains showed that the sequence order was similar.6.Compared with the cpDNA sequence of quinoa samples in GenBank,no significant difference was found in the IRb-LSC region boundary.Among them,the quinoa sequence ycf1 gene with the sequence number MF805727 did not cross the SSC-IRa boundary.Mauve alighment for synteny analysis of cpDNA genomes of different strains showed that the complete chloroplast gene sequence of different quinoa strains showed a collinearity structure.7.Comparing with the cpDNA sequences of other species in Chenopodiaceae in GenBank and analyzing the IR boundary,the results showed that most species have no large-scale variations and changes in boundary regions.There are a few gene rearrangements among several species;13 different quinoa species in this study have ectopic inversions in the atp B to trn V-UAC gene clusters;the trnl-GAU gene and trn A-UGC gene of B.vulgaris species were lost;the trn G-UCC gene of D.ambrosioides species of Chenopodiaceae was lost.Like other species in Chenopodiaceae,the trnl-GAU and trn A-UGC genes of Haloxylon persicum and Haloxylon ammodendron were located between rrn23 and rrn16 genes,but the coding direction is opposite.8.Using Amaranthus caudatus and Amaranthus tricolor from the family Amaranthaceae as outgroups,the ML phylogenetic tree of 41 species in eight genera of Chenopodiaceae was established based on the combined sequence of protein coding genes.The results highly supported the monophyly of eight genera,and spinacia and Chenopodium,Haloxylon and Salicornia are sister groups,respectively,with 100% support value.In addition,twenty species from Chenopodium formed two big branches,and C.quinoa and C.album are sister species.In this study,we used the next-generation sequencing technology to obtain the complete chloroplast genome sequence of 13 quinoa strains.We compared and analyzed the sequence composition and structural characteristics of the complete chloroplast genome sequence of different strains,and combined with GenBank data of Chenopodiaceae species to construct the phylogentic tree to examine the shrinkage and expansion of the chloroplast genome boundary positions,to explore gene rearrangements and deletions,and application among genera of Chenopodiaceae and quinoa strains.