To examine the composition of genes and study the occurring evolutionary processes, researchers generally extract genes in the mitochondrial region rather than genes in the cell nucleus. As we know, at the time of cell division, the cell nucleus which is initially diploid (2n) will be divided in half with genetic components which will also be divided into two (n).
In gamete cells (egg and sperm cells) with haploid properties (n), the merging of the two cells will produce a combination that has characteristics which are not 100% the same as the parent (both father and mother) which means it returns to diploid cells (2n). Whereas in mitochondrial cells, the composition of existing genes, is passed on without experiencing reductions as in gonad cells.
In egg division, only mitochondrial organelles that do not change and are passed on to the next generation, so the decay and evolutionary process of a vertebrate organism, in particular, can be studied through genes in the mitochondria. In this paper we will describe the composition of genes in green shrimp.
Green Shrimp Biology
Green shrimp or Chlorotocus crassicornis (Costa, 1871), is one of the shrimps that live deep at sea depths around 200 ~ 400m. This green shrimp was first identified in the waters of the Mediterranean Sea and the Atlantic Ocean, Almeria Canyon, and then some other publications mentioned that the shrimp had been distributed quite widely from the Mediterranean Sea to the Western Indo-Pacific.
This species plays an essential ecological role as benthic animals as predators and at the same time as prey. This research is the first report on the complete mitochondrial genome of species C. crassicornis green shrimp that has been registered in the GenBank database with accession number NC 035828.
The latest generation of sequencing application
Chlorotocus crassicornis shrimp samples were obtained from the East China Sea waters (123.5 ° E and 34.5 ° N), and the specimens were stored at the National Institute of Fisheries Science (NIFS), Korea. The mitochondrial genome was obtained by combining two fragments of Polymerase Chain Reaction (PCR) that were quite large using the extended PCR technique. The PCR process is a process of doubling DNA strands through a reaction that involves several enzymes under certain temperature conditions and is carried out with a specified duration of time according to the target amount of DNA desired.
The PCR results were then collected together and fragmented into smaller sizes (around 350 base pairs). For large quantities procurement processes, Next Generation Sequencing (NGS) uses the Illumina Miseq platform by conducting DNA library using the TruSeq® RNA V2 library kit that follows the guidelines given by the company.
The NGS method is the latest sequencing method that allows getting very large DNA sequences. It has developed with the support of computer technology and the development of Big Data analysis, which is currently becoming a trend in the development of science and technology.
Composition of Green Shrimp Gene
The complete mitochondrial genome of C. crassicornis has a length of 16,500 base pairs, which is similar to its relatives in its family, Pandalopsis japonica and Pandalus borealis. This mitogenome has an arrangement that consists of 22 transfer RNA (tRNA), two ribosomal RNA (12S and 16S), 13 protein-coding genes, and putative control region (D-Loop).
From the 37 genes, 23 genes (9 protein-coding genes, and 14 tRNA) were encoded in High-strand (H) whose transcriptions go counter-clockwise while the remaining 14 genes (two rRNA, ND1, ND4, ND4L, ND5, and 8 tRNA genes) are located in Light-strand (L) which in the process of protein transcription go clockwise.
All tRNAs owned are predicted to be able to form a folded three-leaf clover structure, except for the Ser-tRNA. Codon start is not determined in the COX1 region, similar to other shrimp groups (crustaceans) as in Pleoticus muellerii shrimp species, with a typical start codon, ATG started in six Protein-coding genes, PCG (COX2, ATP6, COX3, ND4, ND4L, and Cyt b). The incomplete stop codon (TA- / T–) was also detected in five genes, including COX1, COX2, ND5, ND4, and Cytb.
Green Shrimp Pedigree Tree
The genealogical tree (phylogenetic) with the selection of a minimum evolutionary algorithm of 14 species in the Pleocyemata suborder was built based on 13 protein-coding genes. The phylogenetic tree clearly shows that C. crassicornis is closest to Pandalopsis japonica with 77% identity. This mitogenomic information is very useful in C. crassicornis phylogenetic studies and marine fisheries resource management strategies in Korean waters. (*)
Author : Sapto Andriyono
Detailed information from the results of this study can be found in scientific journals at the following link:
https://www.tandfonline.com/doi/pdf/10.1080/23802359.2019.1624633?needAccess=true
