On Theoretical Models of Gene Expression Evolution with Random Genetic Drift and Natural Selection

The relative contributions of natural selection and random genetic drift are a major source of debate in the study of gene expression evolution, which is hypothesized to serve as a bridge from molecular to phenotypic evolution. It has been suggested that the conflict between views is caused by the lack of a definite model of the neutral hypothesis, which can describe the long-run behavior of evolutionary change in mRNA abundance. Therefore previous studies have used inadequate analogies with the neutral prediction of other phenomena, such as amino acid or nucleotide sequence evolution, as the null hypothesis of their statistical inference.In this study, we introduced two novel theoretical models, one based on neutral drift and the other assuming natural selection, by focusing on a common property of the distribution of mRNA abundance among a variety of eukaryotic cells, which reflects the result of long-term evolution. Our results demonstrated that (1) our models can reproduce two independently found phenomena simultaneously: the time development of gene expression divergence and Zipf's law of the transcriptome; (2) cytological constraints can be explicitly formulated to describe long-term evolution; (3) the model assuming that natural selection optimized relative mRNA abundance was more consistent with previously published observations than the model of optimized absolute mRNA abundances.The models introduced in this study give a formulation of evolutionary change in the mRNA abundance of each gene as a stochastic process, on the basis of previously published observations. This model provides a foundation for interpreting observed data in studies of gene expression evolution, including identifying an adequate time scale for discriminating the effect of natural selection from that of random genetic drift of selectively neutral variations

BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression

BodyMap-Xs () is a database for cross-species gene expression comparison. It was created by the anatomical breakdown of 17 million animal expressed sequence tag (EST) records in DDBJ using a sorting program tailored for this purpose. In BodyMap-Xs, users are allowed to compare the expression patterns of orthologous and paralogous genes in a coherent manner. This will provide valuable insights for the evolutionary study of gene expression and identification of a responsive motif for a particular expression pattern. In addition, starting from a concise overview of the taxonomical and anatomical breakdown of all animal ESTs, users can navigate to obtain gene expression ranking of a particular tissue in a particular animal. This method may lead to the understanding of the similarities and differences between the homologous tissues across animal species. BodyMap-Xs will be automatically updated in synchronization with the major update in DDBJ, which occurs periodically

Gene expression profile of renal proximal tubules regulated by proteinuria

Gene expression profile of renal proximal tubules regulated by proteinuria.BackgroundProximal tubules activated by reabsorption of protein are thought to play significant roles in the progression of kidney diseases. Thus, identification of genes related to proteinuria should provide insights into the pathological process of tubulointerstitial fibrosis.MethodGene expression profiles were constructed by means of direct sequencing procedures to identify genes induced in the mouse kidney proximal tubules (PT) exposed to proteinuria.ResultsBy comparing the gene expression of control PT to that of disease model PT, the abundantly expressed genes in control PT were down-regulated presumably because of potentially toxic effects of proteinuria. From the more than 1000 up-regulated genes, an immunity related gene, thymic shared antigen-1 (TSA-1), and a novel gene, GS188, were selected for further characterization. The increased expression of TSA-1, a member of the Ly-6 family, and of GS188 in response to proteinuria was confirmed by Northern analysis, immunohistochemistry, in situ hybridization and laser microdissection along with real-time PCR analysis. Full length cloning of GS188 identified it as a family member of LR8 that was reported to express predominantly in fibroblasts.ConclusionsThe gene expression profiles showed that the expression patterns in PT were changed dramatically by proteinuria. The profiles include novel genes that should be further characterized to aid the understanding of the pathophysiology of progressive kidney diseases

DDBJ launches a new archive database with analytical tools for next-generation sequence data

The DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) has collected and released 1 701 110 entries/1 116 138 614 bases between July 2008 and June 2009. A few highlighted data releases from DDBJ were the complete genome sequence of an endosymbiont within protist cells in the termite gut and Cap Analysis Gene Expression tags for human and mouse deposited from the Functional Annotation of the Mammalian cDNA consortium. In this period, we started a novel user announcement service using Really Simple Syndication (RSS) to deliver a list of data released from DDBJ on a daily basis. Comprehensive visualization of a DDBJ release data was attempted by using a word cloud program. Moreover, a new archive for sequencing data from next-generation sequencers, the ‘DDBJ Read Archive’ (DRA), was launched. Concurrently, for read data registered in DRA, a semi-automatic annotation tool called the ‘DDBJ Read Annotation Pipeline’ was released as a preliminary step. The pipeline consists of two parts: basic analysis for reference genome mapping and de novo assembly and high-level analysis of structural and functional annotations. These new services will aid users’ research and provide easier access to DDBJ databases

The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms

The Human Anatomic Gene Expression Library (H-ANGEL) is a resource for information concerning the anatomical distribution and expression of human gene transcripts. The tool contains protein expression data from multiple platforms that has been associated with both manually annotated full-length cDNAs from H-InvDB and RefSeq sequences. Of the H-Inv predicted genes, 18 897 have associated expression data generated by at least one platform. H-ANGEL utilizes categorized mRNA expression data from both publicly available and proprietary sources. It incorporates data generated by three types of methods from seven different platforms. The data are provided to the user in the form of a web-based viewer with numerous query options. H-ANGEL is updated with each new release of cDNA and genome sequence build. In future editions, we will incorporate the capability for expression data updates from existing and new platforms. H-ANGEL is accessible at http://www.jbirc.aist.go.jp/hinv/h-angel/

ミトコンドリア オヨビ マイクロサテライト DNA タケイ ニ モトヅク アバシリ エミュー シュウダン ノ イデンテキ コウゾウ

エミュー(Dromaius novaehollandiae)はオーストラリア原産の走鳥類であり,エミューオイル,食肉および卵などを生産することから,オホーツク地域の新規産業動物として期待されている。しかし,エミューの生産形質における遺伝的改良はほとんど実施されておらず,それは今後のオホーツクにおけるエミュー産業の発展に必須となることが予測される。我々はミトコンドリアDNA(mtDNA)およびマイクロサテライトDNA多型を指標として,網走におけるエミュー集団の遺伝的多様性を調査した。D-loop領域の塩基配列を決定し,23個体間において比較した結果,2ヶ所の塩基置換サイトが検出され,2種類のハプロタイプの存在が認められた(a-ハプロタイプ:15792C/16114Gおよびb-ハプロタイプ:15792T/16114A)。それらの頻度は,それぞれ0.96および0.04であり,網走集団の多くはa-ハプロタイプに占められていた。一方,4座位のマイクロサテライトDNAについて83個体のジェノタイピングを行った結果,そのすべてにおいて多型が認められ,平均アレル数は7.25,平均ヘテロ接合率は 0.52(H_O)および0.59(H_E)であった。したがって,網走におけるエミュー集団は高い遺伝的多様性を保持することが示唆された。The emu (Dromaius novaehollandiae) is a ratite native to Australia. Various products, including oils, meat, and eggs, can be obtained from the emu, making it a useful industrial animal. The genetic improvement of the emu is essential for the development of emu farming. To estimate the genetic diversity of the domestic emu population in Abashiri, we investigated mitochondrial DNA (mtDNA) and microsatellite DNA polymorphisms. The D-loop region of mtDNA was sequenced, and two haplotypes were detected: 15792C/16114G (a-haplotype) and 15792T/16114A (b-haplotype), with respective frequencies of 0.96 and 0.04. Therefore, the a-haplotype was overwhelmingly prevalent in the Abashiri population. Additionally, four microsatellite loci were genotyped, and polymorphism was detected at all markers. The average number of alleles at these markers was 7.25, and the average observed heterozygosity (H_O) was 0.52, compared to an average expected heterozygosity (H_E) of 0.59. Therefore, we speculated that high genetic diversity was maintained in the Abashiri emu population

マイクロサテライト ブンセキ ニ モトヅク ニホン ノ エミュー シヨウ シュウダン ニ オケル イデンテキ タヨウド

エミュー（Dromaius novaehollandiae）は食肉，卵およびオイルを生産する新規動物資源となることが期待されている。しかしながら，エミュー産業の歴史は浅く，その生産形質の遺伝的改良はほとんど進んでいない。我々は，日本で最大規模となる北海道網走市のエミュー牧場の個体群を対象としてマイクロサテライト解析に基づく遺伝的多様度を経年的に調査した。検出されたアレルの数（NA）は2013，2014，2015および2016年でそれぞれ4.83，4.17，4.17および7.17であり，ヘテロ接合率（HE/HO）はそれぞれ0.466/0.339，0.426/0.325，0.433/0.384および0.550/0.347であった。近交係数（FIS）は調査したすべての世代において正の値を示し，2016年に孵化した個体では0.369と最も高い値が観察された。Structureプログラムを用いた解析では，本集団は3つのクラスターに分かれ，2016年に孵化した個体群は明らかに他の世代とは異なる遺伝的構成を示した。またアレル共有率に基づく系統樹は5つのクレードを示し，2016年に孵化した個体の約半数は一つのクレードに属した。本研究は，網走市のエミュー集団は遺伝的多様度が低いこと，遺伝的に3－5の異なる系統から構成されること，ならびに2016年に孵化した個体の遺伝的構成が他の世代とは異なることを確認した。The emu (Dromaius novaehollandiae) is predicted to be a new livestock animal for oil, meat and egg production. However, the genetic structure of emu populations in Japanese farms is scarcely known. The aim of this study was to determine the genetic diversity and population structure in the largest emu farm in Japan. We collected feather pulps of emu chicks (N＝131) from 40, 20, 23, and 48 individuals hatched at 2013, 2014, 2015, and 2016, respectively, in the Okhotsk Emu farm in Abashiri, Hokkaido, Japan. Using six microsatellite markers, we investigated the genetic diversity and structure of this farmed emu population. The number of alleles (NA) were 4.83, 4.17, 4.17, and 7.17, in individuals hatched in 2013, 2014, 2015, and 2016, respectively. Expected and observed heterozygosity (HE ; HO, respectively) was 0.466/0.339, 0.426/0.325, 0.433/0.384, and 0.550/0.347, in each year, respectively. A high inbreeding coefficient (FIS) was observed in all tested generations (0.113-0.369). The Structure program and unrooted phylogenetic tree analysis showed that the Abashiri emu population is largely divided into three to five different clades. Our results suggested that the genetic diversity in the Abashiri emu population is low, and that it contains three to five genetic lineages. These data may help guide a more sustainable breeding of emus in Japan

Bat fauna in the “Okhotsk Forest”, Koshitoshi, Abashiri City, Hokkaido

北海道網走市の「オホーツクの森」において，コウモリ類の分布および生態を調査した。調査期間は2019 年 7 月 23 日から 2021 年 9 月 27 日とし，調査地点は 30 地点を設定した。捕獲調査の結果，8 種 152 頭のコウモリ類を捕獲した。網走市で初確認となるニホンウサギコウモリ，テングコウモリを捕獲し，網走市には 10 種のコウモリが生息していることが明らかとなった。チチブコウモリ，ヒメホオヒゲコウモリ，コテングコウモリが捕獲数の 89.3% を占めており，特にチチブコウモリが多く捕獲された。チチブコウモリの生息には，ねぐらとなる針葉樹および主食となる蛾の宿主である広葉樹が関係していると考えられた。また，5 種のコウモリから妊娠時の腹部の膨らみや授乳痕を確認し，出産哺育が行われていることが判明した。 外灯調査により，ダム天端の外灯を利用するコウモリの存在が確認された。「オホーツクの森」中心部の調査地点 3 地点において，チチブコウモリの妊娠および出産哺育個体 6 頭を捕獲した。調査開始直後に捕獲されたことから，調査地点周辺にチチブコウモリの出産哺育コロニーが存在していたと考えられる。We investigated the distribution and ecology of bats in the “Okhotsk Forest” in Abashiri City, Hokkaido. The survey period for the study was from July 23, 2019, to September 27, 2021. Thirty survey points were set and 152 bats of eight species were captured. Plecotus sacrimontis and Murina hilgendorfi were the first bats discovered in this area, and 10 species of bats have been reported in Abashiri City. Barbastella darjelingensis, Myotis ikonnikovi, and Murina ussuriensis accounted for 89.3% of the captured bats, and B. darjelingensis was captured the most. The presence of coniferous trees, which are used for roosting, and broadleaf trees that host moths, which are their staple food, were thought to be related to the habitat of B. darjelingensis. Swelling of the abdomen and nursing marks during pregnancy were confirmed in five species of bats, suggesting that childbirth and child-rearing were being performed. A survey near the outdoor lights at the crest of the dam confirmed its use by bats. Six pregnant and child-rearing animals of the B. darjelingensis were captured at three survey points in the center of “Okhotsk Forest”. Since they were captured immediately after the start of the survey, it is　probable that there were birth and child-rearing colonies of B. darjelingensis near the survey points.E1P論文Articledepartmental bulletin pape