Novel evolutionary insights into nemacheilid cavefi sh: evidence from comparative analysis of mitochondrial genomes

Cavefi sh can be important models for understanding the relationships among evolution,adaptation,and development in extreme environments.However,cavefi sh remain poorly studied,particularly at the genome level.Here,we sequenced the complete mitogenome of three cavefi sh in the family Nemacheilidae(Paranemachilus pingguoensis,Oreonectes polystigmus,and Heminoemacheilus longibarbatus),which were collected from karst caves in South China.The mitogenomes each contained 37 genes(13 protein coding,22 tRNA,and two rRNA genes)and a single control region,with the same genetic arrangement and distribution as those found in vertebrates.The non-synonymous/synonymous mutation ratios(Ka/Ks)of the mitogenomes indicated that the protein-coding genes(PCGs)of the three cavefi sh evolved under purifying selection.The mitogenomes of the three cavefi sh exhibit nucleotide composition biases for PCGs,tRNAs,rRNAs,and the whole genome,indicating that the mitochondrial DNA might have been subjected to evolutionary selection in response to extreme cave environments.Divergence time and evolutionary history analyses suggested that the speciation and diversifi cation of the cavefi sh coincided with the Miocene uplift of the southern Qinghai-Tibet Plateau,which greatly changed cave habitats.Overall,our study sheds light on the mitogenomes,phylogeny,and evolutionary history of nemacheilid cavefi sh.

The ties of brotherhood between japonica and indica rice for regional adaptation

Selection of beneficial genomic variants was crucial for regional adaptation of crops during domestication,but the underlying genomic basis remains largely unexplored.Here we report a genome-wide selective-sweep analysis of 655 japonica and 1,205 indica accessions selected from 2,673 landraces through principal component analysis to identify 5,636 non-synonymous single nucleotide polymorphisms(SNPs)fixed in at least one subspecies.We classified these SNPs into three groups,jiS(japonica-and indica-selected),jS(japonica-selected only),and iS(indica-selected only),and documented evidence for selection acting on these groups,their relation to yield-related traits,such as heading date,and their practical value in cropping area prediction.We also demonstrated the role of a jiS-SNP-containing gene in temperature adaptability.Our study informs genes underpinning adaptation that may shape Green Super Rice and proposes a time-saving,cost-reducing selection strategy of genomic breeding,sweep-SNP-guided selection,for developing regionally-adapted heterosis.

DSDecode： A Web-Based Tool for Decoding of Sequencing Chromatograms for Genotyping of Targeted Mutations

Dear Editor,The transcription activator-like effector nucleases （TALENs） and clustered regularly interspaced short palindromic repeats （CRISPR）/Cas9 genome editing systems have greatly improved the efficiency for generating targeted mutations in various organisms including plants （Li et al., 2012; Cong et al., 2013; Li et al., 2013; Feng et al., 2014; Ma et al., 2015b; Zhang et al., 2014, 2015）. In some plant species, the majority of mutations induced by TALENs and CRISPR/Cas9 systems are in uniform biallelic and heterozygous status in the first transgenic generation, although in some other plant species, chimeric mutations （with three or more allelic edited events within a single individual） may frequently occur （Li et al., 2013; Feng et al., 2014; Zhang et al., 2014, 2015; Ma et al., 2015b）. In many cases, it is necessary to determine the mutated sequences of the targeted alleles. However, direct sequencing （with the Sanger method） of PCR amplicons containing such biallelic or heterozygous mutations results in superimposed sequencing peaks starting from the mutation sites. Therefore, cloning of the mutation- containing amplicons and sequencing of multiple clones for each target editing site are required to determine the mutated sequences of the targeted alleles, which is tedious, time consuming, and expensive. Aimed at this problem, we have recently developed a highly reliable Degenerate Sequence De- coding （DSD） method （Ma et al., 2015a） and applied it to decode hundreds of targeted mutation events in rice and Arabidopsis （Ma et al., 2015b）. The DSD method decodes superimposed sequencing chromatograms in the following steps： （1） starting from the first overlapping-peak position on the chromatogram, manually generate a short degenerate sequence （DS） that is adjacent to the anchor sequence （AS）, which sits upstream of the first overlapping-peak; （2） query the DS against the intact reference sequence twice with a sequence analysis program to find the matched sequence（s）; and （3） link the AS with the query-matched sequences to generate the allele sequences or, if detecting only one matching hit, generate the second allele sequence by subtracting the allele 1 nucleotides from the degenerate bases. Even though simple and highly efficient, manual operation of this DSD method is still time consuming when decoding a large number of superimposed sequencing chromatograms.