Taxonomy of Korean Calanthe species and few of its mutants based on AFLP data

스리칸스,구자춘,구자정,최경,박광우,소순구,최용국,황성수 한국식물분류학회 2012 식물 분류학회지 Vol.42 No.3

Five Korean Calanthe species, C. discolor, C. bicolor, C. sieboldii, C. reflexa, and C. aristulifera, were studied using amplified fragment length polymorphism (AFLP) to assess their taxonomic and genetic relationships. Sixteen accessions belonging to five native Calanthe spp. and mutants with yellow tepal and white lip (YW mutants) were studied. We identified 50 putative markers using AFLP analysis. The results of AMOVA showed that genetic variance was higher between species than within species. Genetic dissimilarity when compared with the rest of the species was the lowest for individuals of the YW mutants and the highest for individuals of C. reflexa. The mutants clustered outside the major group. Calanthe bicolor clustered with C. discolor, suggesting that its genetic composition is closer to that of C. discolor. Though it is suggested to have originated as a result of natural hybridization between C. sieboldii and C. discolor, introgression is likely to have occurred in the direction of C. discolor based on the data of molecular marker, clustering and genetic dissimilarity. Calanthe reflexa and C. aristulifera were genetically the most diverse of the species studied. In conclusion, the results showed that there is genetic diversity in Korean Calanthe species, that C. bicolor introgressed in the direction of C. discolor and that the YW mutants are genetically closer to C. sieboldii. Five Korean Calanthe species, C. discolor, C. bicolor, C. sieboldii, C. reflexa, and C. aristulifera, were studied using amplified fragment length polymorphism (AFLP) to assess their taxonomic and genetic relationships. Sixteen accessions belonging to five native Calanthe spp. and mutants with yellow tepal and white lip (YW mutants) were studied. We identified 50 putative markers using AFLP analysis. The results of AMOVA showed that genetic variance was higher between species than within species. Genetic dissimilarity when compared with the rest of the species was the lowest for individuals of the YW mutants and the highest for individuals of C. reflexa. The mutants clustered outside the major group. Calanthe bicolor clustered with C. discolor, suggesting that its genetic composition is closer to that of C. discolor. Though it is suggested to have originated as a result of natural hybridization between C. sieboldii and C. discolor, introgression is likely to have occurred in the direction of C. discolor based on the data of molecular marker, clustering and genetic dissimilarity. Calanthe reflexa and C. aristulifera were genetically the most diverse of the species studied. In conclusion, the results showed that there is genetic diversity in Korean Calanthe species, that C. bicolor introgressed in the direction of C. discolor and that the YW mutants are genetically closer to C. sieboldii.

Genetic relationship of Aloe vera ‘Saengjang’, a new forma, based on cpDNA and ITS sequence variation

크리쉬나모르씨 스리칸스,장선일,황성수 한국식물분류학회 2014 식물 분류학회지 Vol.44 No.4

This study was carried out to understand the genetic relationship of three Aloe spp. cultivated in Korea, A. saponaria, A. vera and A. arborescens and a new variant in Korea based on three plastid (matK, trnLF, rbcL) and one nuclear (ITS regions) DNA barcode markers. A total of 2,420 bp sequence was amplified. Two indels were detected in the trnL region, and also several species specific nucleotide loci were detected in all 29 parsimonious informative sites, and 148 variable sites were detected among four taxa studied while 170 variable and 75 parsimonious sites were detected when other Aloe spp. in worldwide were used. An UPGMA phenogram with 10,000 bootstrap replication showed that the new variant was closest to A. vera. The variant was not morphologically and genetically concurrent with any reported species so far. The clustering of Aloe species were broadly in agreement with previously reported results.

Opuntia humifusa (Raf.) Raf. f. jeollaensis E. J. Kim & S. S. Whang, a new forma based on three DNA markers

김은정,크리쉬나모르씨 스리칸스,이은애,황성수 한국식물분류학회 2014 식물 분류학회지 Vol.44 No.3

The taxonomic status of a new forma, Opuntia humifusa (Raf.) Raf. f. jeollaensis E. J. Kim & S. S. Whang, and the taxonomic relationships of three Korean cladodes were studied based on DNA sequences of three genes. The new forma O. humifusa f. jeollaensis (Wanggasi-Chunnyuncho) is simlilar to O. humifusa (Chunnyuncho), but differ in having both flower with the reddish inner center, and strong and many 3 cm long spines. Molecular studies showed that the new forma grouped into Macrocentra series instead of Humifusa series which included Korean O. humifusa. We designated the new taxa firstly studied here as a new forma, because the taxa have been mainly cultivated in farmlands in Jeolla-do area rather than distributed in nature. The taxonomic relationships of three Korean cladodes are discussed in detail.

기생성 및 포식성 천적에 대한 작물보호제 '비티플러스'의 독성 평가

서삼열,고이구라 스리칸스,권기면,장신애,김용균,Seo, Sam-Yeol,Srikanth, Koigoora,Kwon, Gi-Myon,Jang, Sin-Ae,Kim, Yong-Gyun 한국응용곤충학회 2012 한국응용곤충학회지 Vol.51 No.1

신작물보호제로 개발된 '비티플러스'의 천적에 대한 영향평가가 이뤄졌다. 분석된 천적은 두 종의 기생성 천적인 콜레마니진디벌($Aphidius$ $colemani$) 및 황온좀벌($Eretmocerus$ $eremicus$)과 네 종의 포식성 천적인 무당벌레($Harmonia$ $axyridis$), 애꽃노린재($Orius$ $laevigatus$), 지중해이리 응애($Amblyseius$ $swirskii$) 및 칠레이리응애($Phytoseiulus$ $persimilis$)를 포함했다. '비티플러스'는 세 가지 곤충병원세균($Xenorhabdus$ $nematophila$(Xn), $Photorhabdus$ $temperata$ subsp. $temperata$(Ptt), $Bacillus$ $thuringiensis$(Bt))과 세균 대사물질(BM)을 조합하여 개발되었다. 배추좀나방($Plutella$ $xylostella$) 4령충에 대해서 세 종류의 '비티플러스'('Xn+Bt', 'Ptt+Bt' 그리고 'BM+Bt') 모두는 Bt 단독에 비해 높은 살충력을 나타냈다. '비티플러스'의 천적에 대한 영향에서 세균배양액 혼합체('Xn+Bt' 또는 'Ptt+Bt')는 접촉독성 및 섭식독성 분석에서 모두 독성이 낮은 것으로 나타났다. 그러나 'BM+Bt'는 일부 독성을 보였으며, 특별히 지중해이리응애와 칠레이리응애에 대해서 높은 독성을 나타냈다. 이들 세균대사물질의 살비효과를 점박이응애($Tetranychus$ $urticae$)를 대상으로 분석하였다. 각 대사물질별로 상이한 살비력을 보인 가운데, '비티플러스'에 이용된 대사물질 복합체는 반수치사약량이 218.7 ppm(95% 신뢰구간: 163.2 - 262.3)으로 비교적 높은 살비효과를 나타냈다. 이들 물질의 독성은 Sf9 세포주에 대한 세포독성 분석을 통해 나타났다. 특별히 'BM+Bt' 제조에 사용된 주성분인 벤질리덴아세톤은 낮은 농도에서도 높은 세포독성을 보였다. Effect of a new crop protectant 'Bt-Plus' on natural enemies was analyzed in this study. Tested natural enemies included two parasitic species of $Aphidius$ $colemani$ and $Eretmocerus$ $eremicus$, and four predatory species of $Harmonia$ $axyridis$, $Orius$ $laevigatus$, $Amblyseius$ $swirskii$, and $Phytoseiulus$ $persimilis$. 'Bt-Plus' was formulated by combination of three entomopathogenic bacteria ($Xenorhabdus$ $nematophila$ (Xn), $Photorhabdus$ $temperata$ subsp. $temperata$ (Ptt), $Bacillus$ $thuringiensis$ (Bt)) and bacterial metabolite (BM). All three types of 'Bt-Plus' showed significantly higher toxicities against fourth instar $Plutella$ $xylostella$ larvae than Bt single treatment. Two types of bacterial mixtures ('Xn+Bt' and 'Ptt+Bt') showed little toxicity to all natural enemies in both contact and oral feeding assays. However, 'BM+Bt' showed significant toxicities especially to two predatory mites of $A.$ $swirskii$ and $P.$ $persimilis$. The acaricidal effects of different bacterial metabolites were evaluated against two spotted spider mite, $Tetranychus$ $urticae$. All six BM chemicals showed significant acaricidal effects. The BM mixture used to prepare 'Bt-Plus' showed a high acaricidal activity with a median lethal concentration at 218.7 ppm (95% confidence interval: 163.2 - 262.3). These toxic effects of bacterial metabolites were also proved by cytotoxicity test against Sf9 cells. Especially, benzylideneacetone, which was used as a main ingredient of 'BM+Bt', showed high cytotoxicity at its low micromolar concentration.

일루미나에서 제작된 TSLRH (Truseq Synthetic Long-Read Haplotyping)와 10X Genomics에서 제작된 The Chromium Genome 시퀀싱 플랫폼을 이용하여 생산된 한우(한국 재래 소)의 반수체형 페이징 및 단일염기서열변이 비교 분석

박원철(Woncheoul Park),크리스나무티 스리칸스(Krishnamoorthy Srikanth),박종은(Jong-Eun Park),신동현(Donghyun Shin),고해수(Haesu Ko),임다정(Dajeong Lim),조인철(In-Cheol Cho) 한국생명과학회 2019 생명과학회지 Vol.29 No.1

한우(한국 재래 소)에서 반수체형 페이징을 위한 고밀도 시퀀싱을 이용한 비교 분석 논문은 많지가 않다. 이런 고밀도 시퀀싱 플랫폼 중에서, 일루미나에서 서비스 하는 Truseq Synthetic Long-Read Haplotyping 시퀀싱 플랫폼(TSLRH)과 10X Genomics에서 서비스하는 The Chromium Genome 시퀀싱 플랫폼을 특별히 비교 분석하는 논문은 없다. 우리는 한우 연구소의 한우 종모우(아이디: TN1505D2184 or 27214)의 정액에서 DNA를 추출하였으며, 이 DNA로부터 각각의 시퀀싱 플랫폼을 이용하여 시퀀싱 데이터를 생산하였다. 그 후, 우리는 각각의 시퀀싱 플랫폼에 맞는 분석 방법을 이용하여 단일염기서열변이들은 찾아냈다. 그 결과, TSLRH과 10XG의 전체 리드 수는 각각 355,208,304, 1,632,772,004, 맵핑 리드의 개수는 351,992,768(99.09%), 1,526,641,824(93.50%), Q30(%)은 89.04%, 88.60%, 평균 밀도는 13.04X, 74.3X, 가장 긴 페이즈 블락은 1,982,706bp, 1,480,081 bp, N50 페이즈 블락은 57,637bp, 114,394 bp, 전체 단일염기서열변이는 4,534,989, 8,496,813, 전체 페이징 비율은 72.29%, 87.67%였다. 더욱이, 우리는 각각의 시퀀싱 플랫폼을 비교해서 각각의 시퀀싱 플랫폼의 고유한 단일염기서열변이와 두 시퀀싱 플랫폼에서 공통적으로 존재하는 단일염기서열변이를 각 염색체 별로 확인하였으며, 단일염기서열변이의 개수는 염색체 길이에 정비례한다는 결과를 확인하였다. 결론적으로, 본 연구에서 추천하는 바는 연구비가 충분하지 않을 시에는 TSLRH 보다 10XG을 사용하는 것을 추천한다. 왜냐하면 전체 리드 및 단일염기서열변이 개수, N50 페이즈 블락, 가장 긴 페이즈 블락, 페이즈 비율 그리고 평균 밀도 등이 TSLRH 보다 10XG가 더 높거나 좋기 때문이다. In Hanwoo cattle (Korean native cattle), there is a scarcity of comparative analysis papers using highdepth sequencing and haplotype phasing, particularly a comparative analysis of the Truseq Synthetic Long-Read Haplotyping sequencing platform serviced by Illumina (TSLRH) versus the Chromium Genome Sequencing platform serviced by 10X Genomics (10XG). DNA was extracted from the sperm of a Hanwoo breeding bull (ID: TN1505D2184/27214) provided by Hanwoo research canter and used for the generation of sequence data from both the sequencing platforms. We then identified SNVs using an appropriate analysis pipeline tailored for each platform. The TSLRH and 10XG platforms generated a total of 355,208,304 and 1,632,772,004 reads, respectively, corresponding to a Q30 (%) of 89.04% and 88.60%, respectively, of which 351,992,768(99.09%) and 1,526,641,824(93.50%) were successfully mapped. For the TSLRH and 10XG platforms, the mean depth of the sequencing was 13.04X and 74.3X, the longest phase block was 1,982,706 bp and 1,480,081 bp, the N50 phase block was 57,637 bp and 114,394 bp, the total number of SNVs identified was 4,534,989 and 8,496,813, and the total phased rate was 72.29% and 87.67%, respectively. Moreover, for each chromosome, we identified unique and common SNVs using both sequencing platforms. The number of SNVs was directly proportional to the length of the chromosome. Based on our results, we recommend the use of the 10XG platform for haplotype phasing and SNV identification, as it generated a longer N50 phase block, in addition to a higher mean depth, total number of reads, total number of SNVs, and phase rate, than the TSLRH platform.