Mitogenomic variation in the Black-throated Tit(Aegithalos concinnus):Conserved structure,concerted evolution of duplicate control regions and multiple distinct evolutionary lineages

The mitochondrial genome is a prominent research topic due to its indispensable role in organisms and its application in many research disciplines.However,few studies have investigated intraspecies mitogenomic variation.In this study,69 mitogenomes of the Black-throated Tit(Aegithalos concinnus)were assembled and annotated from a large number of short reads generated using high-throughput sequencing technology.Comparative analyses revealed that mitogenomic characteristics such as length,gene and nucleotide composition,codon usage,and duplicated control regions were relatively conserved despite substantial intraspecies morphological changes.Yet,all the individuals from the subspecies A.c.iredalei had one more nucleotide in the 12S rRNA than the other studied subspecies.Phylogenetic analyses showed five distinct lineages based on the complete mitogenomes and the 13 combined protein-coding genes,whereas only four lineages were observed when using the duplicate control regions.Most interestingly,each lineage had both copies of the control regions of the comprising individuals,indicating that the paralogous control regions were more similar than the orthologous sequences from the distinct lineages.This suggested the control regions had undergone concerted evolution.The Black-throated Tit has complex evolutionary history and needs further investigating the taxonomic status of these lineages,as well as the underlying evolutionary processes.Our findings call for more research on intraspecies mitogenomic variation.

Prospects for discriminating Zingiberaceae species in India using DNA barcodes

We evaluated nine plastid （matK, rbcL, rpoCl, rpoB, rp136-rpsS, ndhJ, trnL-F, tmrnH-psbA, accD） and two nuclear （ITS and ITS2） barcode loci in family Zingiberaceae by analyzing 60 accessions of 20 species belonging to seven genera from India. Bidirectional sequences were recovered for every plastid locus by direct sequencing of polymerase chain reaction （PCR） amplicons in all the accessions tested. However, only 35 （58%） and 4o accessions （66~） yielded ITS and ITS2 sequences, respectively, by direct sequencing. In different bioinformatics analyses, matK and rbcL consistently resolved 15 species （75%） into monophyletic groups and five species into two para- phyletic groups. The 173 ITS sequences, including 138 cloned sequences from 23 accessions, discriminated only 12 species （6o%）, and the remaining species were entered into three paraphyletic groups. Phylogenetic and genealogic analyses of plastid and ITS sequences imply the possible occurrence ofnatural hybridizations in the evolutionary past in giving rise to species paraphyly and intragenomic ITS heterogeneity in the species tested. The results support using matK and rbcL loci for barcoding Zingiberaceae members and highlight the poor utility of iTS and the highly regarded ITS2 in barcoding this family, and also caution against proposing ITS loci for barcoding taxa based on limited sampling.